Read the Docs build information Build id: 417954 Project: institute-for-disease-modeling-emod-api Version: latest Commit: 1ccc2bb2d79c89d4f320f1b9c73dd50746f8037b Date: 2020-09-10T17:19:06.951231Z State: finished Success: True [rtd-command-info] start-time: 2020-09-10T17:19:08.447881Z, end-time: 2020-09-10T17:19:09.381628Z, duration: 0, exit-code: 0 git clone --no-single-branch --depth 50 git@github.com:InstituteforDiseaseModeling/emod-api.git . Cloning into '.'... Warning: Permanently added 'github.com,192.30.255.113' (RSA) to the list of known hosts. [rtd-command-info] start-time: 2020-09-10T17:19:09.901525Z, end-time: 2020-09-10T17:19:10.074960Z, duration: 0, exit-code: 0 git checkout --force origin/master Note: checking out 'origin/master'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by performing another checkout. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example: git checkout -b HEAD is now at 1ccc2bb Updates to fix numpy/scipy dependency errors and make RTD docs live (#90) [rtd-command-info] start-time: 2020-09-10T17:19:10.244571Z, end-time: 2020-09-10T17:19:10.297350Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-09-10T17:19:12.579890Z, end-time: 2020-09-10T17:19:17.591950Z, duration: 5, exit-code: 0 python3.7 -mvirtualenv --system-site-packages Using base prefix '/home/docs/.pyenv/versions/3.7.3' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2020-09-10T17:19:18.331391Z, end-time: 2020-09-10T17:19:19.045705Z, duration: 0, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages (20.2.3) [rtd-command-info] start-time: 2020-09-10T17:19:19.148746Z, end-time: 2020-09-10T17:19:26.993715Z, duration: 7, exit-code: 0 python -m pip install --upgrade --no-cache-dir -I Pygments==2.3.1 setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<1.1 Collecting Pygments==2.3.1 Downloading Pygments-2.3.1-py2.py3-none-any.whl (849 kB) Collecting setuptools==41.0.1 Downloading setuptools-41.0.1-py2.py3-none-any.whl (575 kB) Collecting docutils==0.14 Downloading docutils-0.14-py3-none-any.whl (543 kB) Collecting mock==1.0.1 Downloading mock-1.0.1.tar.gz (818 kB) Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx<2 Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB) Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) Collecting readthedocs-sphinx-ext<1.1 Downloading readthedocs_sphinx_ext-1.0.4-py2.py3-none-any.whl (28 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.8.0-py2.py3-none-any.whl (8.6 MB) Collecting requests>=2.0.0 Downloading requests-2.24.0-py2.py3-none-any.whl (61 kB) Collecting six>=1.5 Downloading six-1.15.0-py2.py3-none-any.whl (10 kB) 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Successfully built mock future Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, pytz, babel, chardet, urllib3, certifi, idna, requests, six, sphinxcontrib-serializinghtml, sphinxcontrib-websupport, pyparsing, packaging, imagesize, snowballstemmer, MarkupSafe, Jinja2, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.8.0 certifi-2020.6.20 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.4 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.1 readthedocs-sphinx-ext-1.0.4 recommonmark-0.5.0 requests-2.24.0 setuptools-50.3.0 six-1.15.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.25.10 [rtd-command-info] start-time: 2020-09-10T17:19:27.215769Z, end-time: 2020-09-10T17:19:41.713431Z, duration: 14, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Collecting sphinx-rtd-theme~=0.5.0 Downloading sphinx_rtd_theme-0.5.0-py2.py3-none-any.whl (10.8 MB) Collecting sphinxcontrib-napoleon~=0.7 Downloading sphinxcontrib_napoleon-0.7-py2.py3-none-any.whl (17 kB) Collecting sphinx~=3.2.1 Downloading Sphinx-3.2.1-py3-none-any.whl (2.9 MB) Collecting plantweb~=1.2.1 Downloading plantweb-1.2.1-py3-none-any.whl (20 kB) Collecting sphinxcontrib-programoutput~=0.16 Downloading sphinxcontrib_programoutput-0.16-py2.py3-none-any.whl (21 kB) Collecting py-make Downloading py_make-0.1.1-py2.py3-none-any.whl (9.4 kB) Collecting PyGithub~=1.51 Downloading PyGithub-1.53-py3-none-any.whl (274 kB) Collecting pygit2~=1.2.1 Downloading pygit2-1.2.1-cp37-cp37m-manylinux2010_x86_64.whl (3.0 MB) Collecting pockets>=0.3 Downloading pockets-0.9.1-py2.py3-none-any.whl (26 kB) Requirement already satisfied: six>=1.5.2 in 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sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (2.0.0) Collecting sphinxcontrib-qthelp Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (50.3.0) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages (from sphinx~=3.2.1->-r docs/requirements.txt (line 3)) (2.3.1) Requirement already satisfied: requests>=2.5.0 in 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docopt (setup.py): started Building wheel for docopt (setup.py): finished with status 'done' Created wheel for docopt: filename=docopt-0.6.2-py2.py3-none-any.whl size=13704 sha256=7c3bfd5596a88eea5cd961d293737dce7076e72c9067c3269c88d372a31c902f Stored in directory: /tmp/pip-ephem-wheel-cache-fgc93j27/wheels/72/b0/3f/1d95f96ff986c7dfffe46ce2be4062f38ebd04b506c77c81b9 Building wheel for wrapt (setup.py): started Building wheel for wrapt (setup.py): finished with status 'done' Created wheel for wrapt: filename=wrapt-1.12.1-cp37-cp37m-linux_x86_64.whl size=70984 sha256=b22fc169bce0305c01b0076eacb8af1476f1ce0b64177d99a6df34bc948a8400 Stored in directory: /tmp/pip-ephem-wheel-cache-fgc93j27/wheels/62/76/4c/aa25851149f3f6d9785f6c869387ad82b3fd37582fa8147ac6 Successfully built docopt wrapt Installing collected packages: sphinxcontrib-applehelp, sphinxcontrib-qthelp, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-jsmath, sphinx, sphinx-rtd-theme, pockets, sphinxcontrib-napoleon, plantweb, sphinxcontrib-programoutput, docopt, py-make, pyjwt, wrapt, deprecated, PyGithub, cached-property, pycparser, cffi, pygit2 Attempting uninstall: sphinx Found existing installation: Sphinx 1.8.5 Uninstalling Sphinx-1.8.5: Successfully uninstalled Sphinx-1.8.5 Attempting uninstall: sphinx-rtd-theme Found existing installation: sphinx-rtd-theme 0.4.3 Uninstalling sphinx-rtd-theme-0.4.3: Successfully uninstalled sphinx-rtd-theme-0.4.3 Successfully installed PyGithub-1.53 cached-property-1.5.1 cffi-1.14.2 deprecated-1.2.10 docopt-0.6.2 plantweb-1.2.1 pockets-0.9.1 py-make-0.1.1 pycparser-2.20 pygit2-1.2.1 pyjwt-1.7.1 sphinx-3.2.1 sphinx-rtd-theme-0.5.0 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-1.0.3 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-napoleon-0.7 sphinxcontrib-programoutput-0.16 sphinxcontrib-qthelp-1.0.3 wrapt-1.12.1 [rtd-command-info] start-time: 2020-09-10T17:19:41.981092Z, end-time: 2020-09-10T17:19:43.863537Z, duration: 1, exit-code: 0 python ./setup.py install --force running install running bdist_egg running egg_info creating emod_api.egg-info writing emod_api.egg-info/PKG-INFO writing dependency_links to emod_api.egg-info/dependency_links.txt writing requirements to emod_api.egg-info/requires.txt writing top-level names to emod_api.egg-info/top_level.txt writing manifest file 'emod_api.egg-info/SOURCES.txt' reading manifest file 'emod_api.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no directories found matching 'emod_api/tests/data/*' warning: no directories found matching 'emod_api/dtk_tools/serialization/test-data/*' writing manifest file 'emod_api.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py creating build creating build/lib creating build/lib/emod_api copying emod_api/campaign.py -> build/lib/emod_api copying emod_api/schema_to_class.py -> build/lib/emod_api copying emod_api/__init__.py -> build/lib/emod_api copying emod_api/__main__.py -> build/lib/emod_api creating build/lib/emod_api/serialization copying emod_api/serialization/SerializedPopulation.py -> build/lib/emod_api/serialization copying emod_api/serialization/dtkFileTools.py -> build/lib/emod_api/serialization copying emod_api/serialization/__init__.py -> build/lib/emod_api/serialization copying emod_api/serialization/__main__.py -> build/lib/emod_api/serialization copying emod_api/serialization/dtkFileSupport.py -> build/lib/emod_api/serialization copying emod_api/serialization/dtkFileUtility.py -> build/lib/emod_api/serialization creating build/lib/emod_api/tabularoutput copying emod_api/tabularoutput/__init__.py -> build/lib/emod_api/tabularoutput copying emod_api/tabularoutput/__main__.py -> build/lib/emod_api/tabularoutput creating build/lib/emod_api/schema copying emod_api/schema/get_schema.py -> build/lib/emod_api/schema copying emod_api/schema/__init__.py -> build/lib/emod_api/schema copying emod_api/schema/dtk_post_process_schema.py -> build/lib/emod_api/schema copying emod_api/schema/__main__.py -> build/lib/emod_api/schema creating build/lib/emod_api/channelreports copying emod_api/channelreports/__init__.py -> build/lib/emod_api/channelreports copying emod_api/channelreports/channels.py -> build/lib/emod_api/channelreports copying emod_api/channelreports/__main__.py -> build/lib/emod_api/channelreports creating build/lib/emod_api/config copying emod_api/config/from_overrides.py -> build/lib/emod_api/config copying emod_api/config/schema_to_config.py -> build/lib/emod_api/config copying emod_api/config/dtk_pre_process_adhocevents.py -> build/lib/emod_api/config copying emod_api/config/from_poi_and_binary.py -> build/lib/emod_api/config copying emod_api/config/default_from_schema_no_validation.py -> build/lib/emod_api/config copying emod_api/config/dtk_post_process_adhocevents.py -> build/lib/emod_api/config copying emod_api/config/__init__.py -> build/lib/emod_api/config copying emod_api/config/default_from_schema.py -> build/lib/emod_api/config copying emod_api/config/from_schema.py -> build/lib/emod_api/config copying emod_api/config/__main__.py -> build/lib/emod_api/config copying emod_api/config/dtk_pre_process_w5ml.py -> build/lib/emod_api/config creating build/lib/emod_api/weather copying emod_api/weather/__init__.py -> build/lib/emod_api/weather copying emod_api/weather/weather.py -> build/lib/emod_api/weather copying emod_api/weather/__main__.py -> build/lib/emod_api/weather creating build/lib/emod_api/interventions copying emod_api/interventions/__init__.py -> build/lib/emod_api/interventions copying emod_api/interventions/outbreak.py -> build/lib/emod_api/interventions copying emod_api/interventions/import_pressure.py -> build/lib/emod_api/interventions copying emod_api/interventions/__main__.py -> build/lib/emod_api/interventions copying emod_api/interventions/simple_vaccine.py -> build/lib/emod_api/interventions creating build/lib/emod_api/examples copying emod_api/examples/serialized_file_mc_to_sc.py -> build/lib/emod_api/examples copying emod_api/examples/__init__.py -> build/lib/emod_api/examples copying emod_api/examples/weather_file.py -> build/lib/emod_api/examples copying emod_api/examples/insetchart.py -> build/lib/emod_api/examples copying emod_api/examples/spatial_report.py -> build/lib/emod_api/examples creating build/lib/emod_api/migration copying emod_api/migration/__init__.py -> build/lib/emod_api/migration copying emod_api/migration/__main__.py -> build/lib/emod_api/migration copying emod_api/migration/migration.py -> build/lib/emod_api/migration creating build/lib/emod_api/spatialreports copying emod_api/spatialreports/__init__.py -> build/lib/emod_api/spatialreports copying emod_api/spatialreports/spatial.py -> build/lib/emod_api/spatialreports copying emod_api/spatialreports/__main__.py -> build/lib/emod_api/spatialreports creating build/lib/emod_api/demographics copying emod_api/demographics/DemographicsGenerator.py -> build/lib/emod_api/demographics copying emod_api/demographics/demographics.py -> build/lib/emod_api/demographics copying emod_api/demographics/__init__.py -> build/lib/emod_api/demographics copying emod_api/demographics/DemographicsTemplates.py -> build/lib/emod_api/demographics copying emod_api/demographics/__main__.py -> build/lib/emod_api/demographics copying emod_api/demographics/DemographicsInputDataParsers.py -> build/lib/emod_api/demographics copying emod_api/demographics/Node.py -> build/lib/emod_api/demographics copying emod_api/demographics/DemographicsFile.py -> build/lib/emod_api/demographics creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/emod_api creating build/bdist.linux-x86_64/egg/emod_api/serialization copying build/lib/emod_api/serialization/SerializedPopulation.py -> build/bdist.linux-x86_64/egg/emod_api/serialization copying build/lib/emod_api/serialization/dtkFileTools.py -> build/bdist.linux-x86_64/egg/emod_api/serialization copying build/lib/emod_api/serialization/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/serialization copying build/lib/emod_api/serialization/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/serialization copying build/lib/emod_api/serialization/dtkFileSupport.py -> build/bdist.linux-x86_64/egg/emod_api/serialization copying build/lib/emod_api/serialization/dtkFileUtility.py -> build/bdist.linux-x86_64/egg/emod_api/serialization creating build/bdist.linux-x86_64/egg/emod_api/tabularoutput copying build/lib/emod_api/tabularoutput/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/tabularoutput copying build/lib/emod_api/tabularoutput/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/tabularoutput creating build/bdist.linux-x86_64/egg/emod_api/schema copying build/lib/emod_api/schema/get_schema.py -> build/bdist.linux-x86_64/egg/emod_api/schema copying build/lib/emod_api/schema/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/schema copying build/lib/emod_api/schema/dtk_post_process_schema.py -> build/bdist.linux-x86_64/egg/emod_api/schema copying build/lib/emod_api/schema/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/schema copying build/lib/emod_api/campaign.py -> build/bdist.linux-x86_64/egg/emod_api copying build/lib/emod_api/schema_to_class.py -> build/bdist.linux-x86_64/egg/emod_api copying build/lib/emod_api/__init__.py -> build/bdist.linux-x86_64/egg/emod_api creating build/bdist.linux-x86_64/egg/emod_api/channelreports copying build/lib/emod_api/channelreports/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/channelreports copying build/lib/emod_api/channelreports/channels.py -> build/bdist.linux-x86_64/egg/emod_api/channelreports copying build/lib/emod_api/channelreports/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/channelreports creating build/bdist.linux-x86_64/egg/emod_api/config copying build/lib/emod_api/config/from_overrides.py -> build/bdist.linux-x86_64/egg/emod_api/config copying build/lib/emod_api/config/schema_to_config.py -> build/bdist.linux-x86_64/egg/emod_api/config copying build/lib/emod_api/config/dtk_pre_process_adhocevents.py -> build/bdist.linux-x86_64/egg/emod_api/config copying build/lib/emod_api/config/from_poi_and_binary.py -> build/bdist.linux-x86_64/egg/emod_api/config copying build/lib/emod_api/config/default_from_schema_no_validation.py -> build/bdist.linux-x86_64/egg/emod_api/config copying build/lib/emod_api/config/dtk_post_process_adhocevents.py -> build/bdist.linux-x86_64/egg/emod_api/config copying build/lib/emod_api/config/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/config copying build/lib/emod_api/config/default_from_schema.py -> build/bdist.linux-x86_64/egg/emod_api/config copying build/lib/emod_api/config/from_schema.py -> build/bdist.linux-x86_64/egg/emod_api/config copying build/lib/emod_api/config/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/config copying build/lib/emod_api/config/dtk_pre_process_w5ml.py -> build/bdist.linux-x86_64/egg/emod_api/config creating build/bdist.linux-x86_64/egg/emod_api/weather copying build/lib/emod_api/weather/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/weather copying build/lib/emod_api/weather/weather.py -> build/bdist.linux-x86_64/egg/emod_api/weather copying build/lib/emod_api/weather/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/weather creating build/bdist.linux-x86_64/egg/emod_api/interventions copying build/lib/emod_api/interventions/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/interventions copying build/lib/emod_api/interventions/outbreak.py -> build/bdist.linux-x86_64/egg/emod_api/interventions copying build/lib/emod_api/interventions/import_pressure.py -> build/bdist.linux-x86_64/egg/emod_api/interventions copying build/lib/emod_api/interventions/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/interventions copying build/lib/emod_api/interventions/simple_vaccine.py -> build/bdist.linux-x86_64/egg/emod_api/interventions creating build/bdist.linux-x86_64/egg/emod_api/examples copying build/lib/emod_api/examples/serialized_file_mc_to_sc.py -> build/bdist.linux-x86_64/egg/emod_api/examples copying build/lib/emod_api/examples/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/examples copying build/lib/emod_api/examples/weather_file.py -> build/bdist.linux-x86_64/egg/emod_api/examples copying build/lib/emod_api/examples/insetchart.py -> build/bdist.linux-x86_64/egg/emod_api/examples copying build/lib/emod_api/examples/spatial_report.py -> build/bdist.linux-x86_64/egg/emod_api/examples creating build/bdist.linux-x86_64/egg/emod_api/migration copying build/lib/emod_api/migration/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/migration copying build/lib/emod_api/migration/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/migration copying build/lib/emod_api/migration/migration.py -> build/bdist.linux-x86_64/egg/emod_api/migration creating build/bdist.linux-x86_64/egg/emod_api/spatialreports copying build/lib/emod_api/spatialreports/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/spatialreports copying build/lib/emod_api/spatialreports/spatial.py -> build/bdist.linux-x86_64/egg/emod_api/spatialreports copying build/lib/emod_api/spatialreports/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/spatialreports copying build/lib/emod_api/__main__.py -> build/bdist.linux-x86_64/egg/emod_api creating build/bdist.linux-x86_64/egg/emod_api/demographics copying build/lib/emod_api/demographics/DemographicsGenerator.py -> build/bdist.linux-x86_64/egg/emod_api/demographics copying build/lib/emod_api/demographics/demographics.py -> build/bdist.linux-x86_64/egg/emod_api/demographics copying build/lib/emod_api/demographics/__init__.py -> build/bdist.linux-x86_64/egg/emod_api/demographics copying build/lib/emod_api/demographics/DemographicsTemplates.py -> build/bdist.linux-x86_64/egg/emod_api/demographics copying build/lib/emod_api/demographics/__main__.py -> build/bdist.linux-x86_64/egg/emod_api/demographics copying build/lib/emod_api/demographics/DemographicsInputDataParsers.py -> build/bdist.linux-x86_64/egg/emod_api/demographics copying build/lib/emod_api/demographics/Node.py -> build/bdist.linux-x86_64/egg/emod_api/demographics copying build/lib/emod_api/demographics/DemographicsFile.py -> build/bdist.linux-x86_64/egg/emod_api/demographics byte-compiling build/bdist.linux-x86_64/egg/emod_api/serialization/SerializedPopulation.py to SerializedPopulation.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/serialization/dtkFileTools.py to dtkFileTools.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/serialization/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/serialization/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/serialization/dtkFileSupport.py to dtkFileSupport.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/serialization/dtkFileUtility.py to dtkFileUtility.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/tabularoutput/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/tabularoutput/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/schema/get_schema.py to get_schema.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/schema/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/schema/dtk_post_process_schema.py to dtk_post_process_schema.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/schema/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/campaign.py to campaign.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/schema_to_class.py to schema_to_class.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/channelreports/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/channelreports/channels.py to channels.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/channelreports/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/from_overrides.py to from_overrides.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/schema_to_config.py to schema_to_config.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/dtk_pre_process_adhocevents.py to dtk_pre_process_adhocevents.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/from_poi_and_binary.py to from_poi_and_binary.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/default_from_schema_no_validation.py to default_from_schema_no_validation.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/dtk_post_process_adhocevents.py to dtk_post_process_adhocevents.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/default_from_schema.py to default_from_schema.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/from_schema.py to from_schema.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/config/dtk_pre_process_w5ml.py to dtk_pre_process_w5ml.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/weather/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/weather/weather.py to weather.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/weather/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/interventions/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/interventions/outbreak.py to outbreak.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/interventions/import_pressure.py to import_pressure.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/interventions/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/interventions/simple_vaccine.py to simple_vaccine.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/examples/serialized_file_mc_to_sc.py to serialized_file_mc_to_sc.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/examples/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/examples/weather_file.py to weather_file.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/examples/insetchart.py to insetchart.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/examples/spatial_report.py to spatial_report.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/migration/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/migration/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/migration/migration.py to migration.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/spatialreports/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/spatialreports/spatial.py to spatial.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/spatialreports/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/DemographicsGenerator.py to DemographicsGenerator.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/demographics.py to demographics.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/__init__.py to __init__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/DemographicsTemplates.py to DemographicsTemplates.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/__main__.py to __main__.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/DemographicsInputDataParsers.py to DemographicsInputDataParsers.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/Node.py to Node.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/emod_api/demographics/DemographicsFile.py to DemographicsFile.cpython-37.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO copying emod_api.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying emod_api.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying emod_api.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying emod_api.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying emod_api.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO zip_safe flag not set; analyzing archive contents... emod_api.config.__pycache__.from_poi_and_binary.cpython-37: module references __file__ emod_api.examples.__pycache__.insetchart.cpython-37: module references __file__ emod_api.examples.__pycache__.spatial_report.cpython-37: module references __file__ emod_api.examples.__pycache__.weather_file.cpython-37: module references __file__ emod_api.serialization.__pycache__.dtkFileTools.cpython-37: module references __file__ emod_api.serialization.__pycache__.dtkFileUtility.cpython-37: module references __file__ creating dist creating 'dist/emod_api-0.1.27-py3.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Processing emod_api-0.1.27-py3.7.egg creating /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages/emod_api-0.1.27-py3.7.egg Extracting emod_api-0.1.27-py3.7.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages Adding emod-api 0.1.27 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages/emod_api-0.1.27-py3.7.egg Processing dependencies for emod-api==0.1.27 Searching for pyyaml Reading https://pypi.org/simple/pyyaml/ Downloading https://files.pythonhosted.org/packages/64/c2/b80047c7ac2478f9501676c988a5411ed5572f35d1beff9cae07d321512c/PyYAML-5.3.1.tar.gz#sha256=b8eac752c5e14d3eca0e6dd9199cd627518cb5ec06add0de9d32baeee6fe645d Best match: PyYAML 5.3.1 Processing PyYAML-5.3.1.tar.gz Writing /tmp/easy_install-88k784e_/PyYAML-5.3.1/setup.cfg Running PyYAML-5.3.1/setup.py -q bdist_egg --dist-dir /tmp/easy_install-88k784e_/PyYAML-5.3.1/egg-dist-tmp-xv8g9hbp In file included from ext/_yaml.c:596:0: ext/_yaml.h:2:10: fatal error: yaml.h: No such file or directory #include ^~~~~~~~ compilation terminated. Error compiling module, falling back to pure Python zip_safe flag not set; analyzing archive contents... Moving PyYAML-5.3.1-py3.7-linux-x86_64.egg to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages Adding PyYAML 5.3.1 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages/PyYAML-5.3.1-py3.7-linux-x86_64.egg Searching for lz4 Reading https://pypi.org/simple/lz4/ Downloading https://files.pythonhosted.org/packages/28/fd/c414b26c9f76f8dc45fbad92dbec7a2c12ca439434e9877f4140d22cf599/lz4-3.1.0-cp37-cp37m-manylinux1_x86_64.whl#sha256=90d275e08e532a91297fe243041bcc16d4166f84134051580ee181990ae0a3ce Best match: lz4 3.1.0 Processing lz4-3.1.0-cp37-cp37m-manylinux1_x86_64.whl Installing lz4-3.1.0-cp37-cp37m-manylinux1_x86_64.whl to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages writing requirements to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages/lz4-3.1.0-py3.7-linux-x86_64.egg/EGG-INFO/requires.txt Adding lz4 3.1.0 to easy-install.pth file Installed /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages/lz4-3.1.0-py3.7-linux-x86_64.egg Searching for pandas==0.25.3 Best match: pandas 0.25.3 Adding pandas 0.25.3 to easy-install.pth file Using /home/docs/.pyenv/versions/3.7.3/lib/python3.7/site-packages Searching for numpy==1.18.1 Best match: numpy 1.18.1 numpy 1.18.1 is already the active version in easy-install.pth Installing f2py script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/bin Installing f2py3 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/bin Installing f2py3.7 script to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/bin Using /home/docs/.pyenv/versions/3.7.3/lib/python3.7/site-packages Searching for python-dateutil==2.8.1 Best match: python-dateutil 2.8.1 python-dateutil 2.8.1 is already the active version in easy-install.pth Using /home/docs/.pyenv/versions/3.7.3/lib/python3.7/site-packages Searching for pytz==2020.1 Best match: pytz 2020.1 Adding pytz 2020.1 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages Searching for six==1.15.0 Best match: six 1.15.0 Adding six 1.15.0 to easy-install.pth file Using /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emod-api/envs/latest/lib/python3.7/site-packages Finished processing dependencies for emod-api==0.1.27 [rtd-command-info] start-time: 2020-09-10T17:19:45.155945Z, end-time: 2020-09-10T17:19:45.231391Z, duration: 0, exit-code: 0 cat docs/conf.py # -*- coding: utf-8 -*- # # Sphinx Demo docs build configuration file, created by # sphinx-quickstart on Fri Aug 26 16:52:16 2016. # # This file is execfile()d with the current directory set to its # containing dir. # # Note that not all possible configuration values are present in this # autogenerated file. # # All configuration values have a default; values that are commented out # serve to show the default. # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # docs root, use os.path.abspath to make it absolute, like shown here. # import os import subprocess import sys import sphinx_rtd_theme import configparser if sys.platform in ["linux", "darwin"]: subprocess.check_output(["make", "generate-api"], cwd=os.path.dirname(os.path.abspath(__file__))) else: subprocess.check_output(["make.bat", "generate-api"], cwd=os.path.dirname(os.path.abspath(__file__))) # -- General configuration ------------------------------------------------ # If your docs needs a minimal Sphinx version, state it here. # # needs_sphinx = '1.0' # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ 'sphinx.ext.imgmath', 'sphinx.ext.githubpages', 'sphinx.ext.autodoc', 'sphinxcontrib.napoleon', 'sphinx.ext.todo', 'plantweb.directive', 'sphinxcontrib.programoutput' ] plantuml = 'plantweb' autodoc_default_options = { 'member-order': 'bysource', 'members': None, 'exclude-members': '__all__' } autodoc_mock_imports = ['emod_api.dtk_tools'] napoleon_google_docstring = True # napoleon_numpy_docstring = True # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: # # source_suffix = ['.rst', '.md'] source_suffix = '.rst' # The encoding of source files. # # source_encoding = 'utf-8-sig' # The master toctree document. master_doc = 'index' # General information about the project. project = u'EMOD-API' copyright = u'2020, Bill & Melinda Gates Foundation. All rights reserved.' author = u'Institute for Disease Modeling' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # # The short X.Y version. #current_path = os.path.dirname(__file__) #version_path = os.path.join(current_path, '..', '.bumpversion.cfg') #config = configparser.ConfigParser() #config.read(version_path) #version = config['bumpversion']['current_version'] # The full version, including alpha/beta/rc tags. # release = u'1.0' # The language for content autogenerated by Sphinx. Refer to docs # for a list of supported languages. # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. language = None # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: # # today = '' # # Else, today_fmt is used as the format for a strftime call. # # today_fmt = '%B %d, %Y' # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This patterns also effect to html_static_path and html_extra_path exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] # The reST default role (used for this markup: `text`) to use for all # documents. # # default_role = None # If true, '()' will be appended to :func: etc. cross-reference text. # # add_function_parentheses = True # If true, the current module name will be prepended to all description # unit titles (such as .. function::). # # add_module_names = True # If true, sectionauthor and moduleauthor directives will be shown in the # output. They are ignored by default. # # show_authors = False # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' # A list of ignored prefixes for module index sorting. # modindex_common_prefix = [] # If true, keep warnings as "system message" paragraphs in the built documents. # keep_warnings = False # If true, `todo` and `todoList` produce output, else they produce nothing. todo_include_todos = False # RST epilog is added to the end of every topic. Useful for replace # directives to use across the docset. rst_epilog = "\n.. include:: /variables.txt" # -- Options for HTML output ---------------------------------------------- # The theme to use for HTML and HTML Help pages. See the docs for # a list of builtin themes. # html_theme = 'sphinx_rtd_theme' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # docs. # # # html_theme_options = { # } # Add any paths that contain custom themes here, relative to this directory. html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] # The name for this set of Sphinx documents. # " v docs" by default. # # html_title = u'Sphinx Demo v1.0' # A shorter title for the navigation bar. Default is the same as html_title. # # html_short_title = None # The name of an image file (relative to this directory) to place at the top # of the sidebar. # html_logo = "images/IDM_white.png" # The name of an image file (relative to this directory) to use as a favicon of # the docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. # html_favicon = "images/favicon.ico" # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_static'] html_context = { 'css_files': [ '_static/theme_overrides.css' ] } # Add any extra paths that contain custom files (such as robots.txt or # .htaccess) here, relative to this directory. These files are copied # directly to the root of the docs. # # html_extra_path = [] # If not None, a 'Last updated on:' timestamp is inserted at every page # bottom, using the given strftime format. # The empty string is equivalent to '%b %d, %Y'. # # html_last_updated_fmt = None # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. # # html_use_smartypants = True # Custom sidebar templates, maps document names to template names. # # html_sidebars = {} # Additional templates that should be rendered to pages, maps page names to # template names. # # html_additional_pages = {} # If false, no module index is generated. # # html_domain_indices = True # If false, no index is generated. # # html_use_index = True # If true, the index is split into individual pages for each letter. # # html_split_index = False # If true, links to the reST sources are added to the pages. # html_show_sourcelink = False # If true, "Created using Sphinx" is shown in the HTML footer. Default is True. # html_show_sphinx = False # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. # # html_show_copyright = True # If true, an OpenSearch description file will be output, and all pages will # contain a tag referring to it. The value of this option must be the # base URL from which the finished HTML is served. # html_use_opensearch = 'www.idmod.org/docs/' # This is the file name suffix for HTML files (e.g. ".xhtml"). # html_file_suffix = None # Language to be used for generating the HTML full-text search index. # Sphinx supports the following languages: # 'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja' # 'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr', 'zh' # # html_search_language = 'en' # A dictionary with options for the search language support, empty by default. # 'ja' uses this config value. # 'zh' user can custom change `jieba` dictionary path. # # html_search_options = {'type': 'default'} # The name of a javascript file (relative to the configuration directory) that # implements a search results scorer. If empty, the default will be used. # # html_search_scorer = 'scorer.js' # Output file base name for HTML help builder. htmlhelp_basename = 'EMOD-API' # -- Options for LaTeX output --------------------------------------------- latex_elements = { # The paper size ('letterpaper' or 'a4paper'). # # 'papersize': 'letterpaper', # The font size ('10pt', '11pt' or '12pt'). # # 'pointsize': '10pt', # Additional stuff for the LaTeX preamble. # # 'preamble': '', # Latex figure (float) alignment # # 'figure_align': 'htbp', } # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, # author, documentclass [howto, manual, or own class]). latex_documents = [ (master_doc, 'emod-api-docs.tex', u'emod-api', u'Institute for Disease Modeling', 'manual'), ] # The name of an image file (relative to this directory) to place at the top of # the title page. # # latex_logo = None # For "manual" documents, if this is true, then toplevel headings are parts, # not chapters. # # latex_use_parts = False # If true, show page references after internal links. # # latex_show_pagerefs = False # If true, show URL addresses after external links. # # latex_show_urls = False # Documents to append as an appendix to all manuals. # # latex_appendices = [] # It false, will not define \strong, \code, itleref, \crossref ... but only # \sphinxstrong, ..., \sphinxtitleref, ... To help avoid clash with user added # packages. # # latex_keep_old_macro_names = True # If false, no module index is generated. # # latex_domain_indices = True # -- Options for manual page output --------------------------------------- # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ (master_doc, 'emod-api-docs', u'emod-api', [author], 1) ] # If true, show URL addresses after external links. # man_show_urls = True # -- Options for Texinfo output ------------------------------------------- # Grouping the document tree into Texinfo files. List of tuples # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ (master_doc, 'emod-api-docs', u'emod-api', author, 'Institute for Disease Modeling', 'How to use emodpy for disease simulations.', 'Miscellaneous'), ] # Documents to append as an appendix to all manuals. # # texinfo_appendices = [] # If false, no module index is generated. # # texinfo_domain_indices = True # How to display URL addresses: 'footnote', 'no', or 'inline'. # # texinfo_show_urls = 'footnote' # If true, do not generate a @detailmenu in the "Top" node's menu. # # texinfo_no_detailmenu = False # Example configuration for intersphinx: refer to the Python standard library. # intersphinx_mapping = {'https://docs.python.org/': None} ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # import importlib import sys import os.path from six import string_types from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://assets.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ], 'downloads': [ ("pdf", "//docs.idmod.org/_/downloads/emod-api/en/latest/pdf/"), ("html", "//docs.idmod.org/_/downloads/emod-api/en/latest/htmlzip/"), ], 'subprojects': [ ], 'slug': 'institute-for-disease-modeling-emod-api', 'name': u'emod-api', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://docs.idmod.org/projects/emod-api/en/latest/', 'analytics_code': 'UA-87656833-3', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'InstituteforDiseaseModeling', 'proxied_api_host': '/_', 'github_repo': 'emod-api', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': 'UA-87656833-3', 'global_analytics_code': 'UA-17997319-2', 'commit': '1ccc2bb2', } if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2020-09-10T17:19:45.440034Z, end-time: 2020-09-10T17:20:50.165187Z, duration: 64, exit-code: 0 python sphinx-build -T -E -W --keep-going -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v3.2.1 rm: cannot remove 'emod_api_index.rst': No such file or directory rm: cannot remove 'modules.rst': No such file or directory make: [generate-api] Error 1 (ignored) loading translations [en]... done making output directory... done building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 49 source files that are out of date updating environment: [new config] 49 added, 0 changed, 0 removed reading sources... [ 2%] emod_api reading sources... [ 4%] emod_api.campaign reading sources... [ 6%] emod_api.channelreports reading sources... [ 8%] emod_api.channelreports.channels reading sources... [ 10%] emod_api.config reading sources... [ 12%] emod_api.config.default_from_schema reading sources... [ 14%] emod_api.config.default_from_schema_no_validation reading sources... [ 16%] emod_api.config.dtk_post_process_adhocevents reading sources... [ 18%] emod_api.config.dtk_pre_process_adhocevents reading sources... [ 20%] emod_api.config.dtk_pre_process_w5ml reading sources... [ 22%] emod_api.config.from_overrides reading sources... [ 24%] emod_api.config.from_poi_and_binary reading sources... [ 26%] emod_api.config.from_schema reading sources... [ 28%] emod_api.config.schema_to_config emod_api.config.schema_to_config is deprecated. Please use emod_api.config.from_schema. reading sources... [ 30%] emod_api.demographics reading sources... [ 32%] emod_api.demographics.DemographicsFile reading sources... [ 34%] emod_api.demographics.DemographicsGenerator reading sources... [ 36%] emod_api.demographics.DemographicsInputDataParsers reading sources... [ 38%] emod_api.demographics.DemographicsTemplates reading sources... [ 40%] emod_api.demographics.Node reading sources... [ 42%] emod_api.demographics.demographics reading sources... [ 44%] emod_api.examples reading sources... [ 46%] emod_api.examples.insetchart reading sources... [ 48%] emod_api.examples.serialized_file_mc_to_sc reading sources... [ 51%] emod_api.examples.spatial_report reading sources... [ 53%] emod_api.examples.weather_file reading sources... [ 55%] emod_api.interventions reading sources... [ 57%] emod_api.interventions.import_pressure reading sources... [ 59%] emod_api.interventions.outbreak reading sources... [ 61%] emod_api.interventions.simple_vaccine reading sources... [ 63%] emod_api.migration reading sources... [ 65%] emod_api.migration.migration reading sources... [ 67%] emod_api.schema reading sources... [ 69%] emod_api.schema.dtk_post_process_schema reading sources... [ 71%] emod_api.schema.get_schema reading sources... [ 73%] emod_api.schema_to_class reading sources... [ 75%] emod_api.serialization reading sources... [ 77%] emod_api.serialization.SerializedPopulation reading sources... [ 79%] emod_api.serialization.dtkFileSupport reading sources... [ 81%] emod_api.serialization.dtkFileTools reading sources... [ 83%] emod_api.serialization.dtkFileUtility reading sources... [ 85%] emod_api.spatialreports reading sources... [ 87%] emod_api.spatialreports.spatial reading sources... [ 89%] emod_api.tabularoutput reading sources... [ 91%] emod_api.weather reading sources... [ 93%] emod_api.weather.weather reading sources... [ 95%] emod_api_index reading sources... [ 97%] glossary reading sources... [100%] index looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 2%] emod_api writing output... [ 4%] emod_api.campaign writing output... [ 6%] emod_api.channelreports writing output... [ 8%] emod_api.channelreports.channels writing output... [ 10%] emod_api.config writing output... [ 12%] emod_api.config.default_from_schema writing output... [ 14%] emod_api.config.default_from_schema_no_validation writing output... [ 16%] emod_api.config.dtk_post_process_adhocevents writing output... [ 18%] emod_api.config.dtk_pre_process_adhocevents writing output... [ 20%] emod_api.config.dtk_pre_process_w5ml writing output... [ 22%] emod_api.config.from_overrides writing output... [ 24%] emod_api.config.from_poi_and_binary writing output... [ 26%] emod_api.config.from_schema writing output... [ 28%] emod_api.config.schema_to_config writing output... [ 30%] emod_api.demographics writing output... [ 32%] emod_api.demographics.DemographicsFile writing output... [ 34%] emod_api.demographics.DemographicsGenerator writing output... [ 36%] emod_api.demographics.DemographicsInputDataParsers writing output... [ 38%] emod_api.demographics.DemographicsTemplates writing output... [ 40%] emod_api.demographics.Node writing output... [ 42%] emod_api.demographics.demographics writing output... [ 44%] emod_api.examples writing output... [ 46%] emod_api.examples.insetchart writing output... [ 48%] emod_api.examples.serialized_file_mc_to_sc writing output... [ 51%] emod_api.examples.spatial_report writing output... [ 53%] emod_api.examples.weather_file writing output... [ 55%] emod_api.interventions writing output... [ 57%] emod_api.interventions.import_pressure writing output... [ 59%] emod_api.interventions.outbreak writing output... [ 61%] emod_api.interventions.simple_vaccine writing output... [ 63%] emod_api.migration writing output... [ 65%] emod_api.migration.migration writing output... [ 67%] emod_api.schema writing output... [ 69%] emod_api.schema.dtk_post_process_schema writing output... [ 71%] emod_api.schema.get_schema writing output... [ 73%] emod_api.schema_to_class writing output... [ 75%] emod_api.serialization writing output... [ 77%] emod_api.serialization.SerializedPopulation writing output... [ 79%] emod_api.serialization.dtkFileSupport writing output... [ 81%] emod_api.serialization.dtkFileTools writing output... [ 83%] emod_api.serialization.dtkFileUtility writing output... [ 85%] emod_api.spatialreports writing output... [ 87%] emod_api.spatialreports.spatial writing output... [ 89%] emod_api.tabularoutput writing output... [ 91%] emod_api.weather writing output... [ 93%] emod_api.weather.weather writing output... [ 95%] emod_api_index writing output... [ 97%] glossary writing output... [100%] index generating indices... genindex py-modindexdone writing additional pages... search opensearchdone copying static files... ... done copying readthedocs static files... done copying searchtools... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded. The HTML pages are in _build/html. [rtd-command-info] start-time: 2020-09-10T17:20:50.548594Z, end-time: 2020-09-10T17:20:55.738108Z, duration: 5, exit-code: 0 python sphinx-build -T -W --keep-going -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia Running Sphinx v3.2.1 rm: cannot remove 'modules.rst': No such file or directory make: [generate-api] Error 1 (ignored) loading translations [en]... done making output directory... done building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: [new config] 49 added, 0 changed, 0 removed reading sources... [ 2%] emod_api reading sources... [ 4%] emod_api.campaign reading sources... [ 6%] emod_api.channelreports reading sources... [ 8%] emod_api.channelreports.channels reading sources... [ 10%] emod_api.config reading sources... [ 12%] emod_api.config.default_from_schema reading sources... [ 14%] emod_api.config.default_from_schema_no_validation reading sources... [ 16%] emod_api.config.dtk_post_process_adhocevents reading sources... [ 18%] emod_api.config.dtk_pre_process_adhocevents reading sources... [ 20%] emod_api.config.dtk_pre_process_w5ml reading sources... [ 22%] emod_api.config.from_overrides reading sources... [ 24%] emod_api.config.from_poi_and_binary reading sources... [ 26%] emod_api.config.from_schema reading sources... [ 28%] emod_api.config.schema_to_config emod_api.config.schema_to_config is deprecated. Please use emod_api.config.from_schema. reading sources... [ 30%] emod_api.demographics reading sources... [ 32%] emod_api.demographics.DemographicsFile reading sources... [ 34%] emod_api.demographics.DemographicsGenerator reading sources... [ 36%] emod_api.demographics.DemographicsInputDataParsers reading sources... [ 38%] emod_api.demographics.DemographicsTemplates reading sources... [ 40%] emod_api.demographics.Node reading sources... [ 42%] emod_api.demographics.demographics reading sources... [ 44%] emod_api.examples reading sources... [ 46%] emod_api.examples.insetchart reading sources... [ 48%] emod_api.examples.serialized_file_mc_to_sc reading sources... [ 51%] emod_api.examples.spatial_report reading sources... [ 53%] emod_api.examples.weather_file reading sources... [ 55%] emod_api.interventions reading sources... [ 57%] emod_api.interventions.import_pressure reading sources... [ 59%] emod_api.interventions.outbreak reading sources... [ 61%] emod_api.interventions.simple_vaccine reading sources... [ 63%] emod_api.migration reading sources... [ 65%] emod_api.migration.migration reading sources... [ 67%] emod_api.schema reading sources... [ 69%] emod_api.schema.dtk_post_process_schema reading sources... [ 71%] emod_api.schema.get_schema reading sources... [ 73%] emod_api.schema_to_class reading sources... [ 75%] emod_api.serialization reading sources... [ 77%] emod_api.serialization.SerializedPopulation reading sources... [ 79%] emod_api.serialization.dtkFileSupport reading sources... [ 81%] emod_api.serialization.dtkFileTools reading sources... [ 83%] emod_api.serialization.dtkFileUtility reading sources... [ 85%] emod_api.spatialreports reading sources... [ 87%] emod_api.spatialreports.spatial reading sources... [ 89%] emod_api.tabularoutput reading sources... [ 91%] emod_api.weather reading sources... [ 93%] emod_api.weather.weather reading sources... [ 95%] emod_api_index reading sources... [ 97%] glossary reading sources... [100%] index looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done assembling single document... emod_api_index emod_api emod_api.channelreports emod_api.channelreports.channels emod_api.config emod_api.config.default_from_schema emod_api.config.default_from_schema_no_validation emod_api.config.dtk_post_process_adhocevents emod_api.config.dtk_pre_process_adhocevents emod_api.config.dtk_pre_process_w5ml emod_api.config.from_overrides emod_api.config.from_poi_and_binary emod_api.config.from_schema emod_api.config.schema_to_config emod_api.demographics emod_api.demographics.DemographicsFile emod_api.demographics.DemographicsGenerator emod_api.demographics.DemographicsInputDataParsers emod_api.demographics.DemographicsTemplates emod_api.demographics.Node emod_api.demographics.demographics emod_api.examples emod_api.examples.insetchart emod_api.examples.serialized_file_mc_to_sc emod_api.examples.spatial_report emod_api.examples.weather_file emod_api.interventions emod_api.interventions.import_pressure emod_api.interventions.outbreak emod_api.interventions.simple_vaccine emod_api.migration emod_api.migration.migration emod_api.schema emod_api.schema.dtk_post_process_schema emod_api.schema.get_schema emod_api.serialization emod_api.serialization.SerializedPopulation emod_api.serialization.dtkFileSupport emod_api.serialization.dtkFileTools emod_api.serialization.dtkFileUtility emod_api.spatialreports emod_api.spatialreports.spatial emod_api.tabularoutput emod_api.weather emod_api.weather.weather emod_api.campaign emod_api.schema_to_class glossary done writing... done writing additional files... opensearchdone copying static files... ... done copying readthedocs static files... done copying extra files... done dumping object inventory... done build succeeded. The HTML page is in _build/localmedia. [rtd-command-info] start-time: 2020-09-10T17:20:55.882195Z, end-time: 2020-09-10T17:21:01.080473Z, duration: 5, exit-code: 0 python sphinx-build -b latex -D language=en -d _build/doctrees . _build/latex Running Sphinx v3.2.1 rm: cannot remove 'modules.rst': No such file or directory make: [generate-api] Error 1 (ignored) loading translations [en]... done making output directory... done building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: [new config] 49 added, 0 changed, 0 removed reading sources... [ 2%] emod_api reading sources... [ 4%] emod_api.campaign reading sources... [ 6%] emod_api.channelreports reading sources... [ 8%] emod_api.channelreports.channels reading sources... [ 10%] emod_api.config reading sources... [ 12%] emod_api.config.default_from_schema reading sources... [ 14%] emod_api.config.default_from_schema_no_validation reading sources... [ 16%] emod_api.config.dtk_post_process_adhocevents reading sources... [ 18%] emod_api.config.dtk_pre_process_adhocevents reading sources... [ 20%] emod_api.config.dtk_pre_process_w5ml reading sources... [ 22%] emod_api.config.from_overrides reading sources... [ 24%] emod_api.config.from_poi_and_binary reading sources... [ 26%] emod_api.config.from_schema reading sources... [ 28%] emod_api.config.schema_to_config emod_api.config.schema_to_config is deprecated. Please use emod_api.config.from_schema. reading sources... [ 30%] emod_api.demographics reading sources... [ 32%] emod_api.demographics.DemographicsFile reading sources... [ 34%] emod_api.demographics.DemographicsGenerator reading sources... [ 36%] emod_api.demographics.DemographicsInputDataParsers reading sources... [ 38%] emod_api.demographics.DemographicsTemplates reading sources... [ 40%] emod_api.demographics.Node reading sources... [ 42%] emod_api.demographics.demographics reading sources... [ 44%] emod_api.examples reading sources... [ 46%] emod_api.examples.insetchart reading sources... [ 48%] emod_api.examples.serialized_file_mc_to_sc reading sources... [ 51%] emod_api.examples.spatial_report reading sources... [ 53%] emod_api.examples.weather_file reading sources... [ 55%] emod_api.interventions reading sources... [ 57%] emod_api.interventions.import_pressure reading sources... [ 59%] emod_api.interventions.outbreak reading sources... [ 61%] emod_api.interventions.simple_vaccine reading sources... [ 63%] emod_api.migration reading sources... [ 65%] emod_api.migration.migration reading sources... [ 67%] emod_api.schema reading sources... [ 69%] emod_api.schema.dtk_post_process_schema reading sources... [ 71%] emod_api.schema.get_schema reading sources... [ 73%] emod_api.schema_to_class reading sources... [ 75%] emod_api.serialization reading sources... [ 77%] emod_api.serialization.SerializedPopulation reading sources... [ 79%] emod_api.serialization.dtkFileSupport reading sources... [ 81%] emod_api.serialization.dtkFileTools reading sources... [ 83%] emod_api.serialization.dtkFileUtility reading sources... [ 85%] emod_api.spatialreports reading sources... [ 87%] emod_api.spatialreports.spatial reading sources... [ 89%] emod_api.tabularoutput reading sources... [ 91%] emod_api.weather reading sources... [ 93%] emod_api.weather.weather reading sources... [ 95%] emod_api_index reading sources... [ 97%] glossary reading sources... [100%] index looking for now-outdated files... none found pickling environment... done checking consistency... done processing emod-api-docs.tex... index emod_api_index emod_api emod_api.channelreports emod_api.channelreports.channels emod_api.config emod_api.config.default_from_schema emod_api.config.default_from_schema_no_validation emod_api.config.dtk_post_process_adhocevents emod_api.config.dtk_pre_process_adhocevents emod_api.config.dtk_pre_process_w5ml emod_api.config.from_overrides emod_api.config.from_poi_and_binary emod_api.config.from_schema emod_api.config.schema_to_config emod_api.demographics emod_api.demographics.DemographicsFile emod_api.demographics.DemographicsGenerator emod_api.demographics.DemographicsInputDataParsers emod_api.demographics.DemographicsTemplates emod_api.demographics.Node emod_api.demographics.demographics emod_api.examples emod_api.examples.insetchart emod_api.examples.serialized_file_mc_to_sc emod_api.examples.spatial_report emod_api.examples.weather_file emod_api.interventions emod_api.interventions.import_pressure emod_api.interventions.outbreak emod_api.interventions.simple_vaccine emod_api.migration emod_api.migration.migration emod_api.schema emod_api.schema.dtk_post_process_schema emod_api.schema.get_schema emod_api.serialization emod_api.serialization.SerializedPopulation emod_api.serialization.dtkFileSupport emod_api.serialization.dtkFileTools emod_api.serialization.dtkFileUtility emod_api.spatialreports emod_api.spatialreports.spatial emod_api.tabularoutput emod_api.weather emod_api.weather.weather emod_api.campaign emod_api.schema_to_class glossary resolving references... done writing... done copying TeX support files... copying TeX support files... done build succeeded. The LaTeX files are in _build/latex. Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). [rtd-command-info] start-time: 2020-09-10T17:21:01.321882Z, end-time: 2020-09-10T17:21:01.380313Z, duration: 0, exit-code: 0 cat latexmkrc $latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S'; $makeindex = 'makeindex -s python.ist %O -o %D %S'; add_cus_dep( "glo", "gls", 0, "makeglo" ); sub makeglo { return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" ); } [rtd-command-info] start-time: 2020-09-10T17:21:01.530550Z, end-time: 2020-09-10T17:21:17.356580Z, duration: 15, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=institute-for-disease-modeling-emod-api -interaction=nonstopmode Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 4, chunk 1. Subroutine makeglo redefined at (eval 11) line 7, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 4, chunk 1. Latexmk: This is Latexmk, John Collins, 1 January 2015, version: 4.41. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/bin/latexmk line 7482. Rule 'pdflatex': Rules & subrules not known to be previously run: pdflatex Rule 'pdflatex': The following rules & subrules became out-of-date: 'pdflatex' ------------ Run number 1 of rule 'pdflatex' ------------ Latexmk: applying rule 'pdflatex'... ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="institute-for-disease-modeling-emod-api" "emod-api-docs.tex"' ------------ This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./emod-api-docs.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) (./sphinxmessages.sty) Writing index file institute-for-disease-modeling-emod-api.idx (./institute-for-disease-modeling-emod-api.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] [1] [2] [1] [2] Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) Underfull \hbox (badness 10000) in paragraph at lines 221--221 []\T1/ptm/m/it/10 filename: str = None\T1/ptm/m/n/10 , [3] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) Overfull \hbox (82.64464pt too wide) in paragraph at lines 342--342 []\T1/ptm/m/it/10 path_to_schema\T1/pcr/m/n/10 ) Overfull \hbox (47.68495pt too wide) in paragraph at lines 352--352 []\T1/ptm/m/it/10 config\T1/pcr/m/n/10 ) Overfull \hbox (126.96484pt too wide) in paragraph at lines 366--366 []\T1/ptm/m/it/10 config_path\T1/ptm/m/n/10 , Overfull \hbox (103.63463pt too wide) in paragraph at lines 366--366 \T1/ptm/m/it/10 set_fn\T1/ptm/m/n/10 , Overfull \hbox (95.01491pt too wide) in paragraph at lines 366--366 \T1/ptm/m/it/10 con- Overfull \hbox (133.8048pt too wide) in paragraph at lines 366--366 \T1/ptm/m/it/10 fig_out_path\T1/pcr/m/n/10 ) [4] Underfull \hbox (badness 10000) in paragraph at lines 424--424 []\T1/ptm/m/it/10 configjson_path\T1/ptm/m/n/10 , Overfull \hbox (63.52425pt too wide) in paragraph at lines 442--442 []\T1/ptm/m/it/10 start_config_dict\T1/ptm/m/n/10 , Overfull \hbox (71.87448pt too wide) in paragraph at lines 442--442 \T1/ptm/m/it/10 poi_set_param_fn\T1/pcr/m/n/10 ) Overfull \hbox (66.30441pt too wide) in paragraph at lines 451--451 []\T1/ptm/m/it/10 start_config_path\T1/ptm/m/n/10 , Overfull \hbox (71.87448pt too wide) in paragraph at lines 451--451 \T1/ptm/m/it/10 poi_set_param_fn\T1/pcr/m/n/10 ) Overfull \hbox (18.36475pt too wide) in paragraph at lines 460--460 []\T1/ptm/m/it/10 schema_path\T1/ptm/m/n/10 , Overfull \hbox (41.87448pt too wide) in paragraph at lines 460--460 \T1/ptm/m/it/10 poi_set_param_fn\T1/pcr/m/n/10 ) [5] Underfull \hbox (badness 10000) in paragraph at lines 469--469 []\T1/ptm/m/it/10 eradication_path\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 517--519 []\T1/ptm/m/n/10 builder = s2c.SchemaConfigBuilder( Underfull \hbox (badness 10000) in paragraph at lines 526--526 []\T1/ptm/m/it/10 schema_name=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 schema.json\TS1 /ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 526--526 \T1/ptm/m/it/10 model=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 GENERIC_SIM\TS1/ptm/m/i t/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 526--526 \T1/ptm/m/it/10 con-fig_out=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 config.json\TS1/p tm/m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (28.28418pt too wide) in paragraph at lines 537--537 []\T1/ptm/m/it/10 schema_name=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 schema.json\TS1 /ptm/m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (11.09424pt too wide) in paragraph at lines 537--537 \T1/ptm/m/it/10 model=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 GENERIC_SIM\TS1/ptm/m/i t/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 537--537 \T1/ptm/m/it/10 con- Underfull \hbox (badness 10000) in paragraph at lines 537--537 \T1/ptm/m/it/10 fig_out=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 config.json\TS1/ptm/m /it/10 '\T1/ptm/m/n/10 , LaTeX Warning: Hyper reference `emod_api.config.from_schema:emod_api.config.fro m_schema.SchemaConfigBuilder' on page 6 undefined on input line 538. [6] Overfull \hbox (6.87448pt too wide) in paragraph at lines 566--566 []\T1/ptm/m/it/10 demographics_file\T1/pcr/m/n/10 ) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) Overfull \hbox (18.60422pt too wide) in paragraph at lines 615--615 []\T1/ptm/m/it/10 res_in_arcsec\T1/pcr/m/n/10 ) Overfull \hbox (13.07484pt too wide) in paragraph at lines 634--634 []\T1/ptm/m/it/10 nodes\T1/ptm/m/n/10 , Overfull \hbox (5.01491pt too wide) in paragraph at lines 634--634 \T1/ptm/m/it/10 con- Overfull \hbox (12.23463pt too wide) in paragraph at lines 634--634 \T1/ptm/m/it/10 cerns: Overfull \hbox (2.79494pt too wide) in paragraph at lines 634--634 \T1/ptm/m/it/10 Op- Overfull \hbox (457.54115pt too wide) in paragraph at lines 634--634 \T1/ptm/m/it/10 tional[Union[emod_api.dtk_tools.demographics.DemographicsGenera torConcern.DemographicsGeneratorConcern, Overfull \hbox (429.49101pt too wide) in paragraph at lines 634--634 \T1/ptm/m/it/10 List[emod_api.dtk_tools.demographics.DemographicsGeneratorConce rn.DemographicsGeneratorConcern]]] Underfull \hbox (badness 10000) in paragraph at lines 634--634 \T1/ptm/m/it/10 = Overfull \hbox (10.85487pt too wide) in paragraph at lines 634--634 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , Overfull \hbox (84.4637pt too wide) in paragraph at lines 634--634 \T1/ptm/m/it/10 res_in_arcsec=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 custom\TS1/ptm/ m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (115.46402pt too wide) in paragraph at lines 634--634 \T1/ptm/m/it/10 node_id_from_lat_long=False\T1/pcr/m/n/10 ) [7] Underfull \hbox (badness 10000) in paragraph at lines 746--746 []\T1/ptm/m/it/10 df\T1/ptm/m/n/10 , \T1/ptm/m/it/10 de-mo-graph- Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 ics_filename: Op- Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 tional[str] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 con-cerns: Op- Overfull \hbox (379.54115pt too wide) in paragraph at lines 746--746 \T1/ptm/m/it/10 tional[Union[emod_api.dtk_tools.demographics.DemographicsGenera torConcern.DemographicsGeneratorConcern, Overfull \hbox (351.49101pt too wide) in paragraph at lines 746--746 \T1/ptm/m/it/10 List[emod_api.dtk_tools.demographics.DemographicsGeneratorConce rn.DemographicsGeneratorConcern]]] Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Overfull \hbox (6.4637pt too wide) in paragraph at lines 746--746 \T1/ptm/m/it/10 res_in_arcsec=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 custom\TS1/ptm/ m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (30.83415pt too wide) in paragraph at lines 746--746 \T1/ptm/m/it/10 node_id_from_lat_long=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 de-fault_population: Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 int = 1000\T1/ptm/m/n/10 , Overfull \hbox (79.21327pt too wide) in paragraph at lines 746--746 \T1/ptm/m/it/10 load_other_columns_as_attributes=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 tional[List[str]] Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ex- Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 clude_columns: Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 Op-tional[List[str]] Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Overfull \hbox (0.89452pt too wide) in paragraph at lines 746--746 \T1/ptm/m/it/10 nodeid_column_name: Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 Op-tional[str] Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lat-i- Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 str = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 lat\TS1/ptm/m/it/10 '\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 lon-gi- Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 tion_column_name: [8] Overfull \hbox (54.94496pt too wide) in paragraph at lines 761--762 []\T1/pcr/b/n/10 apply. If not specified, we use the DefaultWorldBankEquilibriu mConcern [9] Underfull \hbox (badness 10000) in paragraph at lines 809--809 []\T1/ptm/m/it/10 population_input_file: Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 str\T1/ptm/m/n/10 , \T1/ptm/m/it/10 de-mo-graph- Underfull \hbox (badness 7851) in paragraph at lines 809--809 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 con-cerns: Op- Overfull \hbox (349.54115pt too wide) in paragraph at lines 809--809 \T1/ptm/m/it/10 tional[Union[emod_api.dtk_tools.demographics.DemographicsGenera torConcern.DemographicsGeneratorConcern, Overfull \hbox (321.49101pt too wide) in paragraph at lines 809--809 \T1/ptm/m/it/10 List[emod_api.dtk_tools.demographics.DemographicsGeneratorConce rn.DemographicsGeneratorConcern]]] Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 res_in_arcsec=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 custom\TS1/ptm/ m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (0.83415pt too wide) in paragraph at lines 809--809 \T1/ptm/m/it/10 node_id_from_lat_long=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 de-fault_population: Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 int = 1000\T1/ptm/m/n/10 , Overfull \hbox (49.21327pt too wide) in paragraph at lines 809--809 \T1/ptm/m/it/10 load_other_columns_as_attributes=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 in-clude_columns: Op- Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 tional[List[str]] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 ex-clude_columns: Op- Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 tional[List[str]] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 nodeid_column_name: Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 Op-tional[str] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 lat-i-tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 str = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 lat\TS1/ptm/m/it/10 '\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 lon-gi- Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 str = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 lon\TS1/ptm/m/it/10 '\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 pop-u-la- Underfull \hbox (badness 6236) in paragraph at lines 809--809 \T1/ptm/m/it/10 tion_column_name: str = Overfull \hbox (54.94496pt too wide) in paragraph at lines 824--825 []\T1/pcr/b/n/10 apply. If not specified, we use the DefaultWorldBankEquilibriu mConcern [10] Overfull \hbox (6.3048pt too wide) in paragraph at lines 880--880 []\T1/ptm/m/it/10 lat\T1/ptm/m/n/10 , Overfull \hbox (13.5249pt too wide) in paragraph at lines 880--880 \T1/ptm/m/it/10 long\T1/ptm/m/n/10 , Overfull \hbox (115.34473pt too wide) in paragraph at lines 880--880 \T1/ptm/m/it/10 res=0.008333333333333333\T1/pcr/m/n/10 ) Overfull \hbox (37.09444pt too wide) in paragraph at lines 886--886 []\T1/ptm/m/it/10 nodelist\T1/pcr/m/n/10 ) Overfull \hbox (11.74474pt too wide) in paragraph at lines 892--892 []\T1/ptm/m/it/10 node_info\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 892--892 \T1/ptm/m/it/10 De- Underfull \hbox (badness 10000) in paragraph at lines 892--892 \T1/ptm/m/it/10 moDf\T1/ptm/m/n/10 , Overfull \hbox (91.34473pt too wide) in paragraph at lines 892--892 \T1/ptm/m/it/10 res=0.008333333333333333\T1/pcr/m/n/10 ) Overfull \hbox (71.74474pt too wide) in paragraph at lines 898--898 []\T1/ptm/m/it/10 node_info\T1/ptm/m/n/10 , Overfull \hbox (41.2549pt too wide) in paragraph at lines 898--898 \T1/ptm/m/it/10 ex- Overfull \hbox (118.90427pt too wide) in paragraph at lines 898--898 \T1/ptm/m/it/10 tra_data_columns=[]\T1/ptm/m/n/10 , Overfull \hbox (151.34473pt too wide) in paragraph at lines 898--898 \T1/ptm/m/it/10 res=0.008333333333333333\T1/pcr/m/n/10 ) [11] Overfull \hbox (124.04425pt too wide) in paragraph at lines 949--949 []\T1/ptm/m/it/10 meanAgeAtInfection=2.5\T1/pcr/m/n/10 ) Overfull \hbox (29.24501pt too wide) in paragraph at lines 955--955 []\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 961--961 []\T1/ptm/m/it/10 AgeBins\T1/ptm/m/n/10 , \T1/ptm/m/it/10 Mor- Overfull \hbox (149.88425pt too wide) in paragraph at lines 993--993 []\T1/ptm/m/it/10 CrudeBirthRate=0.04\T1/ptm/m/n/10 , Overfull \hbox (87.57472pt too wide) in paragraph at lines 993--993 \T1/ptm/m/it/10 Crude- Overfull \hbox (79.59486pt too wide) in paragraph at lines 993--993 \T1/ptm/m/it/10 Mor- Overfull \hbox (110.60472pt too wide) in paragraph at lines 993--993 \T1/ptm/m/it/10 tRate=0.02\T1/pcr/m/n/10 ) Overfull \hbox (22.9045pt too wide) in paragraph at lines 1074--1074 []\T1/ptm/m/it/10 nodeid\T1/ptm/m/n/10 , \T1/ptm/m/it/10 res_in_deg=0.041666666 666666664\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1080--1080 []\T1/ptm/m/it/10 lat\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lon\T1/ptm/m/n/10 , Overfull \hbox (9.16464pt too wide) in paragraph at lines 1080--1080 \T1/ptm/m/it/10 res_in_deg=0.041666666666666664\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1086--1086 []\T1/ptm/m/it/10 lat\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lon\T1/ptm/m/n/10 , [12] Underfull \hbox (badness 10000) in paragraph at lines 1115--1116 []\T1/pcr/b/n/10 distribution \T1/ptm/m/n/10 ^^U The se-lected dis-tri-bu-tion (need to come from Underfull \hbox (badness 10000) in paragraph at lines 1136--1137 \T1/ptm/m/n/10 Set the \T1/pcr/m/n/10 ImmunityDistributionFlag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ImmunityDistribution1 \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 1189--1189 []\T1/ptm/m/it/10 filename\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dis-tri-bu- [13] Underfull \hbox (badness 10000) in paragraph at lines 1233--1233 []\T1/ptm/m/it/10 cb\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1259--1259 []\T1/ptm/m/it/10 cb\T1/ptm/m/n/10 , LaTeX Warning: Hyper reference `emod_api.demographics.demographics:emod_api.dem ographics.demographics.set_static_demographics' on page 14 undefined on input l ine 1260. [14] Overfull \hbox (19.2944pt too wide) in paragraph at lines 1309--1309 []\T1/ptm/m/it/10 filename_format\T1/ptm/m/n/10 , Overfull \hbox (3.61461pt too wide) in paragraph at lines 1309--1309 \T1/ptm/m/it/10 core_idx=0\T1/pcr/m/n/10 ) [15] Underfull \hbox (badness 10000) in paragraph at lines 1442--1442 []\T1/ptm/m/it/10 timestep\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file- [16] Overfull \hbox (24.70302pt too wide) in paragraph at lines 1519--1519 []\T1/ptm/m/it/10 path_to_binary\T1/ptm/m/n/10 , \T1/ptm/m/it/10 path_to_write_ schema=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 schema.json\TS1/ptm/m/it/10 '\T1/pcr/m /n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1603--1603 []\T1/ptm/m/it/10 node_id\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1603--1603 \T1/ptm/m/it/10 num- Overfull \hbox (9.63463pt too wide) in paragraph at lines 1603--1603 \T1/ptm/m/it/10 ber_of_ind\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1615--1615 []\T1/ptm/m/it/10 node_id\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1615--1615 \T1/ptm/m/it/10 num- Underfull \hbox (badness 10000) in paragraph at lines 1615--1615 \T1/ptm/m/it/10 ber_of_ind\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1615--1615 \T1/ptm/m/it/10 prop-er-ties\T1/ptm/m/n/10 , Overfull \hbox (45.96484pt too wide) in paragraph at lines 1621--1621 []\T1/ptm/m/it/10 node_id\T1/ptm/m/n/10 , Overfull \hbox (22.35486pt too wide) in paragraph at lines 1621--1621 \T1/ptm/m/it/10 in- Overfull \hbox (22.35486pt too wide) in paragraph at lines 1621--1621 \T1/ptm/m/it/10 di- Overfull \hbox (26.7948pt too wide) in paragraph at lines 1621--1621 \T1/ptm/m/it/10 vid- Overfull \hbox (43.74474pt too wide) in paragraph at lines 1621--1621 \T1/ptm/m/it/10 ual_idx\T1/ptm/m/n/10 , Overfull \hbox (58.84471pt too wide) in paragraph at lines 1621--1621 \T1/ptm/m/it/10 prop_value\T1/ptm/m/n/10 , Overfull \hbox (29.57497pt too wide) in paragraph at lines 1621--1621 \T1/ptm/m/it/10 han- Overfull \hbox (29.46484pt too wide) in paragraph at lines 1621--1621 \T1/ptm/m/it/10 dle\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1627--1627 []\T1/ptm/m/it/10 prop_values\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1627--1627 \T1/ptm/m/it/10 node\T1/ptm/m/n/10 , [17] Underfull \hbox (badness 10000) in paragraph at lines 1642--1642 []\T1/ptm/m/it/10 attribute\T1/ptm/m/n/10 , \T1/ptm/m/it/10 han-dle\T1/ptm/m/n/ 10 , \T1/ptm/m/it/10 fil- Underfull \hbox (badness 10000) in paragraph at lines 1642--1642 \T1/ptm/m/it/10 ter_fct=>\T1/pcr/m/n/10 ) Overfull \hbox (28.96484pt too wide) in paragraph at lines 1676--1676 []\T1/ptm/m/it/10 handle\T1/ptm/m/n/10 , Overfull \hbox (10.35486pt too wide) in paragraph at lines 1676--1676 \T1/ptm/m/it/10 in- Overfull \hbox (14.23474pt too wide) in paragraph at lines 1676--1676 \T1/ptm/m/it/10 fec- Overfull \hbox (17.3048pt too wide) in paragraph at lines 1676--1676 \T1/ptm/m/it/10 tion\T1/ptm/m/n/10 , Overfull \hbox (55.52435pt too wide) in paragraph at lines 1676--1676 \T1/ptm/m/it/10 fct=>\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1684--1684 []\T1/ptm/m/it/10 suid\T1/ptm/m/n/10 , \T1/ptm/m/it/10 kwargs={}\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1684--1684 \T1/ptm/m/it/10 copy_ind=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1704--1704 []\T1/ptm/m/it/10 name\T1/ptm/m/n/10 , \T1/ptm/m/it/10 han-dle\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cur- Underfull \hbox (badness 10000) in paragraph at lines 1710--1710 []\T1/ptm/m/it/10 handle\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cur- Overfull \hbox (5.06378pt too wide) in paragraph at lines 1710--1710 \T1/ptm/m/it/10 rentlevel=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 dtk.nodes\TS1/ptm/m /it/10 '\T1/pcr/m/n/10 ) [18] Underfull \hbox (badness 6493) in paragraph at lines 1808--1808 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 byte-count\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunkcount\TS1/ptm/m/it/10 '\T1/ptm/m/it/ 10 : Underfull \hbox (badness 10000) in paragraph at lines 1808--1808 \T1/ptm/m/it/10 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunk-sizes\TS1/ptm/m/it/1 0 '\T1/ptm/m/it/10 : [], \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 com- Underfull \hbox (badness 6575) in paragraph at lines 1808--1808 \T1/ptm/m/it/10 10 17:20:59 2020\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 , \TS1/ptm/m/ it/10 '\T1/ptm/m/it/10 en-gine\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : LaTeX Warning: Hyper reference `emod_api.serialization.dtkFileSupport:emod_api. serialization.dtkFileSupport.SerialObject' on page 19 undefined on input line 1 809. [19] Underfull \hbox (badness 10000) in paragraph at lines 1924--1924 []\T1/ptm/m/it/10 header={\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 author\TS1/ptm/m/it /10 '\T1/ptm/m/it/10 : \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 un-known\TS1/ptm/m/it/ 10 '\T1/ptm/m/it/10 , Underfull \hbox (badness 6493) in paragraph at lines 1924--1924 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 byte-count\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunkcount\TS1/ptm/m/it/10 '\T1/ptm/m/it/ 10 : Underfull \hbox (badness 10000) in paragraph at lines 1924--1924 \T1/ptm/m/it/10 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunk-sizes\TS1/ptm/m/it/1 0 '\T1/ptm/m/it/10 : [], \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 com- Underfull \hbox (badness 6575) in paragraph at lines 1924--1924 \T1/ptm/m/it/10 10 17:20:59 2020\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 , \TS1/ptm/m/ it/10 '\T1/ptm/m/it/10 en-gine\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : Underfull \hbox (badness 10000) in paragraph at lines 1924--1924 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 ver-sion\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 1 }\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file-name=\TS1/ptm/m/it/10 ''\T1/ptm/m/n/10 , LaTeX Warning: Hyper reference `emod_api.serialization.dtkFileTools:emod_api.se rialization.dtkFileTools.DtkFile' on page 20 undefined on input line 1925. Underfull \hbox (badness 10000) in paragraph at lines 1938--1938 []\T1/ptm/m/it/10 header={\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 author\TS1/ptm/m/it /10 '\T1/ptm/m/it/10 : \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 un-known\TS1/ptm/m/it/ 10 '\T1/ptm/m/it/10 , Underfull \hbox (badness 6493) in paragraph at lines 1938--1938 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 byte-count\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunkcount\TS1/ptm/m/it/10 '\T1/ptm/m/it/ 10 : Underfull \hbox (badness 10000) in paragraph at lines 1938--1938 \T1/ptm/m/it/10 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunk-sizes\TS1/ptm/m/it/1 0 '\T1/ptm/m/it/10 : [], \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 com- Underfull \hbox (badness 6575) in paragraph at lines 1938--1938 \T1/ptm/m/it/10 10 17:20:59 2020\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 , \TS1/ptm/m/ it/10 '\T1/ptm/m/it/10 en-gine\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : Underfull \hbox (badness 10000) in paragraph at lines 1938--1938 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 ver-sion\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 1 }\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file-name=\TS1/ptm/m/it/10 ''\T1/ptm/m/n/10 , LaTeX Warning: Hyper reference `emod_api.serialization.dtkFileTools:emod_api.se rialization.dtkFileTools.DtkFile' on page 20 undefined on input line 1939. Underfull \hbox (badness 10000) in paragraph at lines 1960--1960 []\T1/ptm/m/it/10 header={\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 author\TS1/ptm/m/it /10 '\T1/ptm/m/it/10 : \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 un-known\TS1/ptm/m/it/ 10 '\T1/ptm/m/it/10 , Underfull \hbox (badness 6493) in paragraph at lines 1960--1960 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 byte-count\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunkcount\TS1/ptm/m/it/10 '\T1/ptm/m/it/ 10 : Underfull \hbox (badness 10000) in paragraph at lines 1960--1960 \T1/ptm/m/it/10 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunk-sizes\TS1/ptm/m/it/1 0 '\T1/ptm/m/it/10 : [], \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 com- Underfull \hbox (badness 6575) in paragraph at lines 1960--1960 \T1/ptm/m/it/10 10 17:20:59 2020\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 , \TS1/ptm/m/ it/10 '\T1/ptm/m/it/10 en-gine\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : Underfull \hbox (badness 10000) in paragraph at lines 1960--1960 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 ver-sion\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 1 }\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file-name=\TS1/ptm/m/it/10 ''\T1/ptm/m/n/10 , LaTeX Warning: Hyper reference `emod_api.serialization.dtkFileTools:emod_api.se rialization.dtkFileTools.DtkFile' on page 20 undefined on input line 1961. 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[20] [21] [22] [23] Underfull \hbox (badness 10000) in paragraph at lines 2389--2391 []\T1/ptm/m/n/10 python -m Underfull \hbox (badness 10000) in paragraph at lines 2392--2394 []\T1/ptm/m/n/10 python -m [24] Chapter 2. [25] [26] LaTeX Warning: Reference `emod_api:module-emod_api' on page 27 undefined on inp ut line 2438. LaTeX Warning: Reference `emod_api.campaign:module-emod_api.campaign' on page 2 7 undefined on input line 2439. LaTeX Warning: Reference `emod_api.channelreports:module-emod_api.channelreport s' on page 27 undefined on input line 2440. LaTeX Warning: Reference `emod_api.channelreports.channels:module-emod_api.chan nelreports.channels' on page 27 undefined on input line 2441. LaTeX Warning: Reference `emod_api.config:module-emod_api.config' on page 27 un defined on input line 2442. LaTeX Warning: Reference `emod_api.config.default_from_schema:module-emod_api.c onfig.default_from_schema' on page 27 undefined on input line 2443. 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(rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on institute-for-disease-modeling-emod-api.pdf (31 pages, 171087 bytes). Transcript written on institute-for-disease-modeling-emod-api.log. Latexmk: Index file 'institute-for-disease-modeling-emod-api.idx' was written Latexmk: Missing input file: 'institute-for-disease-modeling-emod-api.ind' from line 'No file institute-for-disease-modeling-emod-api.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'institute-for-disease-modeling-emod-api.pdf' Latexmk: Log file says output to 'institute-for-disease-modeling-emod-api.pdf' Latexmk: List of undefined refs and citations: Reference `emod_api.campaign:module-emod_api.campaign' on page 27 undefined on input line 2439 Reference `emod_api.channelreports.channels:module-emod_api.channelreports.channels' on page 27 undefined on input line 2441 Reference `emod_api.channelreports:module-emod_api.channelreports' on page 27 undefined on input line 2440 Reference `emod_api.config.default_from_schema:module-emod_api.config.default_from_schema' on page 27 undefined on input line 2443 Reference `emod_api.config.default_from_schema_no_validation:module-emod_api.config.default_from_schema_no_validation' on page 27 undefined on input line 2444 Reference `emod_api.config.dtk_post_process_adhocevents:module-emod_api.config.dtk_post_process_adhocevents' on page 27 undefined on input line 2445 Reference `emod_api.config.dtk_pre_process_adhocevents:module-emod_api.config.dtk_pre_process_adhocevents' on page 27 undefined on input line 2446 Reference `emod_api.config.dtk_pre_process_w5ml:module-emod_api.config.dtk_pre_process_w5ml' on page 27 undefined on input line 2447 Reference `emod_api.config.from_overrides:module-emod_api.config.from_overrides' on page 27 undefined on input line 2448 Reference `emod_api.config.from_poi_and_binary:module-emod_api.config.from_poi_and_binary' on page 27 undefined on input line 2449 Reference `emod_api.config.from_schema:module-emod_api.config.from_schema' on page 27 undefined on input line 2450 Reference `emod_api.config.schema_to_config:module-emod_api.config.schema_to_config' on page 27 undefined on input line 2451 Reference `emod_api.config:module-emod_api.config' on page 27 undefined on input line 2442 Reference `emod_api.demographics.DemographicsFile:module-emod_api.demographics.DemographicsFile' on page 27 undefined on input line 2454 Reference `emod_api.demographics.DemographicsGenerator:module-emod_api.demographics.DemographicsGenerator' on page 27 undefined on input line 2455 Reference `emod_api.demographics.DemographicsInputDataParsers:module-emod_api.demographics.DemographicsInputDataParsers' on page 27 undefined on input line 2456 Reference `emod_api.demographics.DemographicsTemplates:module-emod_api.demographics.DemographicsTemplates' on page 27 undefined on input line 2457 Reference `emod_api.demographics.Node:module-emod_api.demographics.Node' on page 27 undefined on input line 2458 Reference `emod_api.demographics.demographics:module-emod_api.demographics.demographics' on page 27 undefined on input line 2453 Reference `emod_api.demographics:module-emod_api.demographics' on page 27 undefined on input line 2452 Reference `emod_api.examples.insetchart:module-emod_api.examples.insetchart' on page 27 undefined on input line 2460 Reference `emod_api.examples.serialized_file_mc_to_sc:module-emod_api.examples.serialized_file_mc_to_sc' on page 27 undefined on input line 2461 Reference `emod_api.examples.spatial_report:module-emod_api.examples.spatial_report' on page 27 undefined on input line 2462 Reference `emod_api.examples.weather_file:module-emod_api.examples.weather_file' on page 27 undefined on input line 2463 Reference `emod_api.examples:module-emod_api.examples' on page 27 undefined on input line 2459 Reference `emod_api.interventions.import_pressure:module-emod_api.interventions.import_pressure' on page 27 undefined on input line 2465 Reference `emod_api.interventions.outbreak:module-emod_api.interventions.outbreak' on page 27 undefined on input line 2466 Reference `emod_api.interventions.simple_vaccine:module-emod_api.interventions.simple_vaccine' on page 27 undefined on input line 2467 Reference `emod_api.interventions:module-emod_api.interventions' on page 27 undefined on input line 2464 Reference `emod_api.migration.migration:module-emod_api.migration.migration' on page 27 undefined on input line 2469 Reference `emod_api.migration:module-emod_api.migration' on page 27 undefined on input line 2468 Reference `emod_api.schema.dtk_post_process_schema:module-emod_api.schema.dtk_post_process_schema' on page 27 undefined on input line 2471 Reference `emod_api.schema.get_schema:module-emod_api.schema.get_schema' on page 27 undefined on input line 2472 Reference `emod_api.schema:module-emod_api.schema' on page 27 undefined on input line 2470 Reference `emod_api.schema_to_class:module-emod_api.schema_to_class' on page 27 undefined on input line 2473 Reference `emod_api.serialization.SerializedPopulation:module-emod_api.serialization.SerializedPopulation' on page 27 undefined on input line 2478 Reference `emod_api.serialization.dtkFileSupport:module-emod_api.serialization.dtkFileSupport' on page 27 undefined on input line 2475 Reference `emod_api.serialization.dtkFileTools:module-emod_api.serialization.dtkFileTools' on page 27 undefined on input line 2476 Reference `emod_api.serialization.dtkFileUtility:module-emod_api.serialization.dtkFileUtility' on page 27 undefined on input line 2477 Reference `emod_api.serialization:module-emod_api.serialization' on page 27 undefined on input line 2474 Reference `emod_api.spatialreports.spatial:module-emod_api.spatialreports.spatial' on page 27 undefined on input line 2480 Reference `emod_api.spatialreports:module-emod_api.spatialreports' on page 27 undefined on input line 2479 Reference `emod_api.tabularoutput:module-emod_api.tabularoutput' on page 27 undefined on input line 2481 Reference `emod_api.weather.weather:module-emod_api.weather.weather' on page 27 undefined on input line 2483 Reference `emod_api.weather:module-emod_api.weather' on page 27 undefined on input line 2482 Reference `emod_api:module-emod_api' on page 27 undefined on input line 2438 Latexmk: Summary of warnings: Latex failed to resolve 46 reference(s) Rule 'makeindex institute-for-disease-modeling-emod-api.idx': File changes, etc: Non-existent destination files: 'institute-for-disease-modeling-emod-api.ind' ------------ Run number 1 of rule 'makeindex institute-for-disease-modeling-emod-api.idx' ------------ Latexmk: applying rule 'makeindex institute-for-disease-modeling-emod-api.idx'... ------------ Running 'makeindex -s python.ist -o "institute-for-disease-modeling-emod-api.ind" "institute-for-disease-modeling-emod-api.idx"' ------------ This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file institute-for-disease-modeling-emod-api.idx....done (334 entries accepted, 0 rejected). Sorting entries.....done (2897 comparisons). Generating output file institute-for-disease-modeling-emod-api.ind....done (650 lines written, 0 warnings). Output written in institute-for-disease-modeling-emod-api.ind. Transcript written in institute-for-disease-modeling-emod-api.ilg. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'institute-for-disease-modeling-emod-api.aux' 'institute-for-disease-modeling-emod-api.ind' ------------ Run number 2 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="institute-for-disease-modeling-emod-api" "emod-api-docs.tex"' ------------ Latexmk: applying rule 'pdflatex'... 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(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) (./sphinxmessages.sty) Writing index file institute-for-disease-modeling-emod-api.idx (./institute-for-disease-modeling-emod-api.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./institute-for-disease-modeling-emod-api.out) (./institute-for-disease-modeling-emod-api.out) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] (./institute-for-disease-modeling-emod-api.toc) [1] [2] [1] [2] Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) Underfull \hbox (badness 10000) in paragraph at lines 221--221 []\T1/ptm/m/it/10 filename: str = None\T1/ptm/m/n/10 , [3] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) Overfull \hbox (82.64464pt too wide) in paragraph at lines 342--342 []\T1/ptm/m/it/10 path_to_schema\T1/pcr/m/n/10 ) Overfull \hbox (47.68495pt too wide) in paragraph at lines 352--352 []\T1/ptm/m/it/10 config\T1/pcr/m/n/10 ) Overfull \hbox (126.96484pt too wide) in paragraph at lines 366--366 []\T1/ptm/m/it/10 config_path\T1/ptm/m/n/10 , Overfull \hbox (103.63463pt too wide) in paragraph at lines 366--366 \T1/ptm/m/it/10 set_fn\T1/ptm/m/n/10 , Overfull \hbox (95.01491pt too wide) in paragraph at lines 366--366 \T1/ptm/m/it/10 con- Overfull \hbox (133.8048pt too wide) in paragraph at lines 366--366 \T1/ptm/m/it/10 fig_out_path\T1/pcr/m/n/10 ) [4] Underfull \hbox (badness 10000) in paragraph at lines 424--424 []\T1/ptm/m/it/10 configjson_path\T1/ptm/m/n/10 , Overfull \hbox (63.52425pt too wide) in paragraph at lines 442--442 []\T1/ptm/m/it/10 start_config_dict\T1/ptm/m/n/10 , Overfull \hbox (71.87448pt too wide) in paragraph at lines 442--442 \T1/ptm/m/it/10 poi_set_param_fn\T1/pcr/m/n/10 ) Overfull \hbox (66.30441pt too wide) in paragraph at lines 451--451 []\T1/ptm/m/it/10 start_config_path\T1/ptm/m/n/10 , Overfull \hbox (71.87448pt too wide) in paragraph at lines 451--451 \T1/ptm/m/it/10 poi_set_param_fn\T1/pcr/m/n/10 ) Overfull \hbox (18.36475pt too wide) in paragraph at lines 460--460 []\T1/ptm/m/it/10 schema_path\T1/ptm/m/n/10 , Overfull \hbox (41.87448pt too wide) in paragraph at lines 460--460 \T1/ptm/m/it/10 poi_set_param_fn\T1/pcr/m/n/10 ) [5] Underfull \hbox (badness 10000) in paragraph at lines 469--469 []\T1/ptm/m/it/10 eradication_path\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 517--519 []\T1/ptm/m/n/10 builder = s2c.SchemaConfigBuilder( Underfull \hbox (badness 10000) in paragraph at lines 526--526 []\T1/ptm/m/it/10 schema_name=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 schema.json\TS1 /ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 526--526 \T1/ptm/m/it/10 model=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 GENERIC_SIM\TS1/ptm/m/i t/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 526--526 \T1/ptm/m/it/10 con-fig_out=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 config.json\TS1/p tm/m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (28.28418pt too wide) in paragraph at lines 537--537 []\T1/ptm/m/it/10 schema_name=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 schema.json\TS1 /ptm/m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (11.09424pt too wide) in paragraph at lines 537--537 \T1/ptm/m/it/10 model=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 GENERIC_SIM\TS1/ptm/m/i t/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 537--537 \T1/ptm/m/it/10 con- Underfull \hbox (badness 10000) in paragraph at lines 537--537 \T1/ptm/m/it/10 fig_out=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 config.json\TS1/ptm/m /it/10 '\T1/ptm/m/n/10 , [6] Overfull \hbox (6.87448pt too wide) in paragraph at lines 566--566 []\T1/ptm/m/it/10 demographics_file\T1/pcr/m/n/10 ) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) Overfull \hbox (18.60422pt too wide) in paragraph at lines 615--615 []\T1/ptm/m/it/10 res_in_arcsec\T1/pcr/m/n/10 ) Overfull \hbox (13.07484pt too wide) in paragraph at lines 634--634 []\T1/ptm/m/it/10 nodes\T1/ptm/m/n/10 , Overfull \hbox (5.01491pt too wide) in paragraph at lines 634--634 \T1/ptm/m/it/10 con- Overfull \hbox (12.23463pt too wide) in paragraph at lines 634--634 \T1/ptm/m/it/10 cerns: Overfull \hbox (2.79494pt too wide) in paragraph at lines 634--634 \T1/ptm/m/it/10 Op- Overfull \hbox (457.54115pt too wide) in paragraph at lines 634--634 \T1/ptm/m/it/10 tional[Union[emod_api.dtk_tools.demographics.DemographicsGenera torConcern.DemographicsGeneratorConcern, Overfull \hbox (429.49101pt too wide) in paragraph at lines 634--634 \T1/ptm/m/it/10 List[emod_api.dtk_tools.demographics.DemographicsGeneratorConce rn.DemographicsGeneratorConcern]]] Underfull \hbox (badness 10000) in paragraph at lines 634--634 \T1/ptm/m/it/10 = Overfull \hbox (10.85487pt too wide) in paragraph at lines 634--634 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , Overfull \hbox (84.4637pt too wide) in paragraph at lines 634--634 \T1/ptm/m/it/10 res_in_arcsec=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 custom\TS1/ptm/ m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (115.46402pt too wide) in paragraph at lines 634--634 \T1/ptm/m/it/10 node_id_from_lat_long=False\T1/pcr/m/n/10 ) [7] Underfull \hbox (badness 10000) in paragraph at lines 746--746 []\T1/ptm/m/it/10 df\T1/ptm/m/n/10 , \T1/ptm/m/it/10 de-mo-graph- Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 ics_filename: Op- Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 tional[str] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 con-cerns: Op- Overfull \hbox (379.54115pt too wide) in paragraph at lines 746--746 \T1/ptm/m/it/10 tional[Union[emod_api.dtk_tools.demographics.DemographicsGenera torConcern.DemographicsGeneratorConcern, Overfull \hbox (351.49101pt too wide) in paragraph at lines 746--746 \T1/ptm/m/it/10 List[emod_api.dtk_tools.demographics.DemographicsGeneratorConce rn.DemographicsGeneratorConcern]]] Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Overfull \hbox (6.4637pt too wide) in paragraph at lines 746--746 \T1/ptm/m/it/10 res_in_arcsec=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 custom\TS1/ptm/ m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (30.83415pt too wide) in paragraph at lines 746--746 \T1/ptm/m/it/10 node_id_from_lat_long=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 de-fault_population: Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 int = 1000\T1/ptm/m/n/10 , Overfull \hbox (79.21327pt too wide) in paragraph at lines 746--746 \T1/ptm/m/it/10 load_other_columns_as_attributes=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 tional[List[str]] Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ex- Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 clude_columns: Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 Op-tional[List[str]] Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Overfull \hbox (0.89452pt too wide) in paragraph at lines 746--746 \T1/ptm/m/it/10 nodeid_column_name: Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 Op-tional[str] Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lat-i- Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 str = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 lat\TS1/ptm/m/it/10 '\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 lon-gi- Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 tion_column_name: [8] Overfull \hbox (54.94496pt too wide) in paragraph at lines 761--762 []\T1/pcr/b/n/10 apply. If not specified, we use the DefaultWorldBankEquilibriu mConcern [9] Underfull \hbox (badness 10000) in paragraph at lines 809--809 []\T1/ptm/m/it/10 population_input_file: Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 str\T1/ptm/m/n/10 , \T1/ptm/m/it/10 de-mo-graph- Underfull \hbox (badness 7851) in paragraph at lines 809--809 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 con-cerns: Op- Overfull \hbox (349.54115pt too wide) in paragraph at lines 809--809 \T1/ptm/m/it/10 tional[Union[emod_api.dtk_tools.demographics.DemographicsGenera torConcern.DemographicsGeneratorConcern, Overfull \hbox (321.49101pt too wide) in paragraph at lines 809--809 \T1/ptm/m/it/10 List[emod_api.dtk_tools.demographics.DemographicsGeneratorConce rn.DemographicsGeneratorConcern]]] Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 res_in_arcsec=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 custom\TS1/ptm/ m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (0.83415pt too wide) in paragraph at lines 809--809 \T1/ptm/m/it/10 node_id_from_lat_long=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 de-fault_population: Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 int = 1000\T1/ptm/m/n/10 , Overfull \hbox (49.21327pt too wide) in paragraph at lines 809--809 \T1/ptm/m/it/10 load_other_columns_as_attributes=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 in-clude_columns: Op- Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 tional[List[str]] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 ex-clude_columns: Op- Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 tional[List[str]] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 nodeid_column_name: Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 Op-tional[str] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 lat-i-tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 str = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 lat\TS1/ptm/m/it/10 '\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 lon-gi- Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 str = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 lon\TS1/ptm/m/it/10 '\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 pop-u-la- Underfull \hbox (badness 6236) in paragraph at lines 809--809 \T1/ptm/m/it/10 tion_column_name: str = Overfull \hbox (54.94496pt too wide) in paragraph at lines 824--825 []\T1/pcr/b/n/10 apply. If not specified, we use the DefaultWorldBankEquilibriu mConcern [10] Overfull \hbox (6.3048pt too wide) in paragraph at lines 880--880 []\T1/ptm/m/it/10 lat\T1/ptm/m/n/10 , Overfull \hbox (13.5249pt too wide) in paragraph at lines 880--880 \T1/ptm/m/it/10 long\T1/ptm/m/n/10 , Overfull \hbox (115.34473pt too wide) in paragraph at lines 880--880 \T1/ptm/m/it/10 res=0.008333333333333333\T1/pcr/m/n/10 ) Overfull \hbox (37.09444pt too wide) in paragraph at lines 886--886 []\T1/ptm/m/it/10 nodelist\T1/pcr/m/n/10 ) Overfull \hbox (11.74474pt too wide) in paragraph at lines 892--892 []\T1/ptm/m/it/10 node_info\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 892--892 \T1/ptm/m/it/10 De- Underfull \hbox (badness 10000) in paragraph at lines 892--892 \T1/ptm/m/it/10 moDf\T1/ptm/m/n/10 , Overfull \hbox (91.34473pt too wide) in paragraph at lines 892--892 \T1/ptm/m/it/10 res=0.008333333333333333\T1/pcr/m/n/10 ) Overfull \hbox (71.74474pt too wide) in paragraph at lines 898--898 []\T1/ptm/m/it/10 node_info\T1/ptm/m/n/10 , Overfull \hbox (41.2549pt too wide) in paragraph at lines 898--898 \T1/ptm/m/it/10 ex- Overfull \hbox (118.90427pt too wide) in paragraph at lines 898--898 \T1/ptm/m/it/10 tra_data_columns=[]\T1/ptm/m/n/10 , Overfull \hbox (151.34473pt too wide) in paragraph at lines 898--898 \T1/ptm/m/it/10 res=0.008333333333333333\T1/pcr/m/n/10 ) [11] Overfull \hbox (124.04425pt too wide) in paragraph at lines 949--949 []\T1/ptm/m/it/10 meanAgeAtInfection=2.5\T1/pcr/m/n/10 ) Overfull \hbox (29.24501pt too wide) in paragraph at lines 955--955 []\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 961--961 []\T1/ptm/m/it/10 AgeBins\T1/ptm/m/n/10 , \T1/ptm/m/it/10 Mor- Overfull \hbox (149.88425pt too wide) in paragraph at lines 993--993 []\T1/ptm/m/it/10 CrudeBirthRate=0.04\T1/ptm/m/n/10 , Overfull \hbox (87.57472pt too wide) in paragraph at lines 993--993 \T1/ptm/m/it/10 Crude- Overfull \hbox (79.59486pt too wide) in paragraph at lines 993--993 \T1/ptm/m/it/10 Mor- Overfull \hbox (110.60472pt too wide) in paragraph at lines 993--993 \T1/ptm/m/it/10 tRate=0.02\T1/pcr/m/n/10 ) Overfull \hbox (22.9045pt too wide) in paragraph at lines 1074--1074 []\T1/ptm/m/it/10 nodeid\T1/ptm/m/n/10 , \T1/ptm/m/it/10 res_in_deg=0.041666666 666666664\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1080--1080 []\T1/ptm/m/it/10 lat\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lon\T1/ptm/m/n/10 , Overfull \hbox (9.16464pt too wide) in paragraph at lines 1080--1080 \T1/ptm/m/it/10 res_in_deg=0.041666666666666664\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1086--1086 []\T1/ptm/m/it/10 lat\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lon\T1/ptm/m/n/10 , [12] Underfull \hbox (badness 10000) in paragraph at lines 1115--1116 []\T1/pcr/b/n/10 distribution \T1/ptm/m/n/10 ^^U The se-lected dis-tri-bu-tion (need to come from Underfull \hbox (badness 10000) in paragraph at lines 1136--1137 \T1/ptm/m/n/10 Set the \T1/pcr/m/n/10 ImmunityDistributionFlag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ImmunityDistribution1 \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 1189--1189 []\T1/ptm/m/it/10 filename\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dis-tri-bu- [13] Underfull \hbox (badness 10000) in paragraph at lines 1233--1233 []\T1/ptm/m/it/10 cb\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1259--1259 []\T1/ptm/m/it/10 cb\T1/ptm/m/n/10 , [14] Overfull \hbox (19.2944pt too wide) in paragraph at lines 1309--1309 []\T1/ptm/m/it/10 filename_format\T1/ptm/m/n/10 , Overfull \hbox (3.61461pt too wide) in paragraph at lines 1309--1309 \T1/ptm/m/it/10 core_idx=0\T1/pcr/m/n/10 ) [15] Underfull \hbox (badness 10000) in paragraph at lines 1442--1442 []\T1/ptm/m/it/10 timestep\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file- [16] Overfull \hbox (24.70302pt too wide) in paragraph at lines 1519--1519 []\T1/ptm/m/it/10 path_to_binary\T1/ptm/m/n/10 , \T1/ptm/m/it/10 path_to_write_ schema=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 schema.json\TS1/ptm/m/it/10 '\T1/pcr/m /n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1603--1603 []\T1/ptm/m/it/10 node_id\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1603--1603 \T1/ptm/m/it/10 num- Overfull \hbox (9.63463pt too wide) in paragraph at lines 1603--1603 \T1/ptm/m/it/10 ber_of_ind\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1615--1615 []\T1/ptm/m/it/10 node_id\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1615--1615 \T1/ptm/m/it/10 num- Underfull \hbox (badness 10000) in paragraph at lines 1615--1615 \T1/ptm/m/it/10 ber_of_ind\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1615--1615 \T1/ptm/m/it/10 prop-er-ties\T1/ptm/m/n/10 , Overfull \hbox (45.96484pt too wide) in paragraph at lines 1621--1621 []\T1/ptm/m/it/10 node_id\T1/ptm/m/n/10 , Overfull \hbox (22.35486pt too wide) in paragraph at lines 1621--1621 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\T1/ptm/m/it/10 han-dle\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cur- Underfull \hbox (badness 10000) in paragraph at lines 1710--1710 []\T1/ptm/m/it/10 handle\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cur- Overfull \hbox (5.06378pt too wide) in paragraph at lines 1710--1710 \T1/ptm/m/it/10 rentlevel=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 dtk.nodes\TS1/ptm/m /it/10 '\T1/pcr/m/n/10 ) [18] Underfull \hbox (badness 6493) in paragraph at lines 1808--1808 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 byte-count\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunkcount\TS1/ptm/m/it/10 '\T1/ptm/m/it/ 10 : Underfull \hbox (badness 10000) in paragraph at lines 1808--1808 \T1/ptm/m/it/10 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunk-sizes\TS1/ptm/m/it/1 0 '\T1/ptm/m/it/10 : [], \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 com- Underfull \hbox (badness 6575) in paragraph at lines 1808--1808 \T1/ptm/m/it/10 10 17:20:59 2020\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 , \TS1/ptm/m/ it/10 '\T1/ptm/m/it/10 en-gine\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : [19] Underfull \hbox (badness 10000) in paragraph at lines 1924--1924 []\T1/ptm/m/it/10 header={\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 author\TS1/ptm/m/it /10 '\T1/ptm/m/it/10 : \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 un-known\TS1/ptm/m/it/ 10 '\T1/ptm/m/it/10 , Underfull \hbox (badness 6493) in paragraph at lines 1924--1924 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 byte-count\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunkcount\TS1/ptm/m/it/10 '\T1/ptm/m/it/ 10 : Underfull \hbox (badness 10000) in paragraph at lines 1924--1924 \T1/ptm/m/it/10 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunk-sizes\TS1/ptm/m/it/1 0 '\T1/ptm/m/it/10 : [], \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 com- Underfull \hbox (badness 6575) in paragraph at lines 1924--1924 \T1/ptm/m/it/10 10 17:20:59 2020\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 , \TS1/ptm/m/ it/10 '\T1/ptm/m/it/10 en-gine\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : Underfull \hbox (badness 10000) in paragraph at lines 1924--1924 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 ver-sion\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 1 }\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file-name=\TS1/ptm/m/it/10 ''\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1938--1938 []\T1/ptm/m/it/10 header={\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 author\TS1/ptm/m/it /10 '\T1/ptm/m/it/10 : \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 un-known\TS1/ptm/m/it/ 10 '\T1/ptm/m/it/10 , Underfull \hbox (badness 6493) in paragraph at lines 1938--1938 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 byte-count\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunkcount\TS1/ptm/m/it/10 '\T1/ptm/m/it/ 10 : Underfull \hbox (badness 10000) in paragraph at lines 1938--1938 \T1/ptm/m/it/10 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunk-sizes\TS1/ptm/m/it/1 0 '\T1/ptm/m/it/10 : [], \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 com- Underfull \hbox (badness 6575) in paragraph at lines 1938--1938 \T1/ptm/m/it/10 10 17:20:59 2020\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 , \TS1/ptm/m/ it/10 '\T1/ptm/m/it/10 en-gine\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : Underfull \hbox (badness 10000) in paragraph at lines 1938--1938 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 ver-sion\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 1 }\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file-name=\TS1/ptm/m/it/10 ''\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1960--1960 []\T1/ptm/m/it/10 header={\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 author\TS1/ptm/m/it /10 '\T1/ptm/m/it/10 : \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 un-known\TS1/ptm/m/it/ 10 '\T1/ptm/m/it/10 , Underfull \hbox (badness 6493) in paragraph at lines 1960--1960 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 byte-count\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunkcount\TS1/ptm/m/it/10 '\T1/ptm/m/it/ 10 : Underfull \hbox (badness 10000) in paragraph at lines 1960--1960 \T1/ptm/m/it/10 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunk-sizes\TS1/ptm/m/it/1 0 '\T1/ptm/m/it/10 : [], \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 com- Underfull \hbox (badness 6575) in paragraph at lines 1960--1960 \T1/ptm/m/it/10 10 17:20:59 2020\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 , \TS1/ptm/m/ it/10 '\T1/ptm/m/it/10 en-gine\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : Underfull \hbox (badness 10000) in paragraph at lines 1960--1960 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 ver-sion\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 1 }\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file-name=\TS1/ptm/m/it/10 ''\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1982--1982 []\T1/ptm/m/it/10 header={\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 author\TS1/ptm/m/it /10 '\T1/ptm/m/it/10 : \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 un-known\TS1/ptm/m/it/ 10 '\T1/ptm/m/it/10 , Underfull \hbox (badness 6493) in paragraph at lines 1982--1982 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 byte-count\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunkcount\TS1/ptm/m/it/10 '\T1/ptm/m/it/ 10 : Underfull \hbox (badness 10000) in paragraph at lines 1982--1982 \T1/ptm/m/it/10 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunk-sizes\TS1/ptm/m/it/1 0 '\T1/ptm/m/it/10 : [], \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 com- Underfull \hbox (badness 6575) in paragraph at lines 1982--1982 \T1/ptm/m/it/10 10 17:20:59 2020\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 , \TS1/ptm/m/ it/10 '\T1/ptm/m/it/10 en-gine\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : Underfull \hbox (badness 10000) in paragraph at lines 1982--1982 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 ver-sion\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 1 }\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file-name=\TS1/ptm/m/it/10 ''\T1/ptm/m/n/10 , [20] [21] [22] [23] Underfull \hbox (badness 10000) in paragraph at lines 2389--2391 []\T1/ptm/m/n/10 python -m Underfull \hbox (badness 10000) in paragraph at lines 2392--2394 []\T1/ptm/m/n/10 python -m [24] Chapter 2. [25] [26] Overfull \hbox (66.6225pt too wide) in paragraph at lines 2444--2445 []\T1/pcr/m/n/10 emod_api.config.default_from_schema_no_validation\T1/ptm/m/n/1 0 , Overfull \hbox (36.6225pt too wide) in paragraph at lines 2445--2446 []\T1/pcr/m/n/10 emod_api.config.dtk_post_process_adhocevents\T1/ptm/m/n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 2446--2447 []\T1/pcr/m/n/10 emod_api.config.dtk_pre_process_adhocevents\T1/ptm/m/n/10 , Overfull \hbox (0.6225pt too wide) in paragraph at lines 2454--2455 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsFile\T1/ptm/m/n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 2455--2456 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 , Overfull \hbox (72.6225pt too wide) in paragraph at lines 2456--2457 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsInputDataParsers\T1/ptm/m/n/ 10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 2457--2458 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 , Overfull \hbox (24.6225pt too wide) in paragraph at lines 2461--2462 []\T1/pcr/m/n/10 emod_api.examples.serialized_file_mc_to_sc\T1/ptm/m/n/10 , Overfull \hbox (0.6225pt too wide) in paragraph at lines 2465--2466 []\T1/pcr/m/n/10 emod_api.interventions.import_pressure\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2467--2468 []\T1/pcr/m/n/10 emod_api.interventions.simple_vaccine\T1/ptm/m/n/10 , Overfull \hbox (6.6225pt too wide) in paragraph at lines 2471--2472 []\T1/pcr/m/n/10 emod_api.schema.dtk_post_process_schema\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2475--2476 []\T1/pcr/m/n/10 emod_api.serialization.dtkFileSupport\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2477--2478 []\T1/pcr/m/n/10 emod_api.serialization.dtkFileUtility\T1/ptm/m/n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 2478--2479 []\T1/pcr/m/n/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 , [27] (./institute-for-disease-modeling-emod-api.ind [28] Overfull \hbox (30.30013pt too wide) in paragraph at lines 9--11 []\T1/pcr/m/n/10 add() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule emod_api.seri alization.SerializedPopulation\T1/ptm/m/n/10 ), Overfull \hbox (123.59949pt too wide) in paragraph at lines 11--13 []\T1/pcr/m/n/10 addInfection() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serial ization.SerializedPopulation.SerializedPopulation Overfull \hbox (8.17026pt too wide) in paragraph at lines 13--15 \T1/ptm/m/it/10 ule emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ) , Underfull \hbox (badness 10000) in paragraph at lines 15--17 []\T1/pcr/m/n/10 AgeStructureUNWPP() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 15--17 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Overfull \hbox (37.49991pt too wide) in paragraph at lines 17--19 []\T1/pcr/m/n/10 append() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializatio n.dtkFileTools.DtkFile.Contents Overfull \hbox (32.4899pt too wide) in paragraph at lines 19--21 []\T1/pcr/m/n/10 append() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializatio n.dtkFileTools.DtkFile.Objects Underfull \hbox (badness 10000) in paragraph at lines 21--23 []\T1/pcr/m/n/10 application() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (7.95116pt too wide) in paragraph at lines 21--23 \T1/ptm/m/it/10 emod_api.config.dtk_post_process_adhocevents\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 23--25 []\T1/pcr/m/n/10 application() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (4.2412pt too wide) in paragraph at lines 23--25 \T1/ptm/m/it/10 emod_api.config.dtk_pre_process_adhocevents\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 25--27 []\T1/pcr/m/n/10 application() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 25--27 \T1/ptm/m/it/10 emod_api.config.dtk_pre_process_w5ml\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 27--29 []\T1/pcr/m/n/10 application() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 27--29 \T1/ptm/m/it/10 emod_api.schema.dtk_post_process_schema\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 29--31 []\T1/pcr/m/n/10 apply_to_defaults_or_nodes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 i n mod-ule Underfull \hbox (badness 10000) in paragraph at lines 31--33 []\T1/pcr/m/n/10 arcsec_to_deg() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (17.1711pt too wide) in paragraph at lines 31--33 \T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 ), Overfull \hbox (62.83089pt too wide) in paragraph at lines 33--35 []\T1/pcr/m/n/10 as_dataframe() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channe lreports.channels.ChannelReport Overfull \hbox (41.61118pt too wide) in paragraph at lines 35--37 []\T1/pcr/m/n/10 as_dictionary() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.chann elreports.channels.Channel Overfull \hbox (37.71117pt too wide) in paragraph at lines 37--39 []\T1/pcr/m/n/10 as_dictionary() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.chann elreports.channels.Header Underfull \hbox (badness 10000) in paragraph at lines 48--49 []\T1/pcr/m/n/10 basicNode() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (23.59027pt too wide) in paragraph at lines 50--52 []\T1/pcr/m/n/10 byte_count() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializ ation.dtkFileTools.DtkFile Underfull \hbox (badness 10000) in paragraph at lines 55--57 []\T1/pcr/m/n/10 changeSusceptibility() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule Underfull \hbox (badness 10000) in paragraph at lines 55--57 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Overfull \hbox (68.83089pt too wide) in paragraph at lines 58--60 []\T1/pcr/m/n/10 channel_names() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.chann elreports.channels.ChannelReport Underfull \hbox (badness 10000) in paragraph at lines 60--62 []\T1/pcr/m/n/10 ChannelReport \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Overfull \hbox (38.83089pt too wide) in paragraph at lines 62--64 []\T1/pcr/m/n/10 channels() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelrep orts.channels.ChannelReport Overfull \hbox (29.59027pt too wide) in paragraph at lines 64--66 []\T1/pcr/m/n/10 chunk_count() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.seriali zation.dtkFileTools.DtkFile Overfull \hbox (29.59027pt too wide) in paragraph at lines 66--68 []\T1/pcr/m/n/10 chunk_sizes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.seriali zation.dtkFileTools.DtkFile Overfull \hbox (36.91025pt too wide) in paragraph at lines 70--72 []\T1/pcr/m/n/10 compress() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializat ion.dtkFileSupport.EllZeeFour Overfull \hbox (21.29066pt too wide) in paragraph at lines 72--74 []\T1/pcr/m/n/10 compress() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializat ion.dtkFileSupport.Snappy Overfull \hbox (50.91016pt too wide) in paragraph at lines 74--76 []\T1/pcr/m/n/10 compress() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializat ion.dtkFileSupport.Uncompressed Underfull \hbox (badness 10000) in paragraph at lines 76--78 []\T1/pcr/m/n/10 compress() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (23.59027pt too wide) in paragraph at lines 78--80 []\T1/pcr/m/n/10 compressed() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializ ation.dtkFileTools.DtkFile Overfull \hbox (29.59027pt too wide) in paragraph at lines 80--82 []\T1/pcr/m/n/10 compression() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.seriali zation.dtkFileTools.DtkFile [29] Underfull \hbox (badness 10000) in paragraph at lines 82--84 []\T1/pcr/m/n/10 ConstantMortality() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 82--84 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Overfull \hbox (46.65079pt too wide) in paragraph at lines 84--86 \T1/ptm/m/it/10 emod_api.demographics.DemographicsInputDataParsers\T1/ptm/m/n/1 0 ), Underfull \hbox (badness 10000) in paragraph at lines 86--87 []\T1/pcr/m/n/10 Coordinate \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 87--89 []\T1/pcr/m/n/10 createIndividual() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 87--89 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Overfull \hbox (12.84114pt too wide) in paragraph at lines 89--91 []\T1/pcr/m/n/10 creation_date() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weath er.weather.Metadata Overfull \hbox (7.47115pt too wide) in paragraph at lines 91--93 []\T1/pcr/m/n/10 creation_date() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weath er.weather.Weather Underfull \hbox (badness 10000) in paragraph at lines 96--98 []\T1/pcr/m/n/10 data() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelreports .channels.Channel Underfull \hbox (badness 10000) in paragraph at lines 98--100 []\T1/pcr/m/n/10 data() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.spatialreports .spatial.SpatialNode Underfull \hbox (badness 10000) in paragraph at lines 104--106 []\T1/pcr/m/n/10 datavalue_count() Underfull \hbox (badness 10000) in paragraph at lines 104--106 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.weather.Metadata prop- Underfull \hbox (badness 10000) in paragraph at lines 106--108 []\T1/pcr/m/n/10 datavalue_count() Underfull \hbox (badness 10000) in paragraph at lines 106--108 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.weather.Weather prop- Underfull \hbox (badness 10000) in paragraph at lines 108--110 []\T1/pcr/m/n/10 date() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization. dtkFileTools.DtkFile Underfull \hbox (badness 10000) in paragraph at lines 110--111 []\T1/pcr/m/n/10 decode() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (10.77174pt too wide) in paragraph at lines 111--113 []\T1/pcr/m/n/10 default_density \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demog raphics.Node.Node Underfull \hbox (badness 10000) in paragraph at lines 113--115 []\T1/pcr/m/n/10 default_population Underfull \hbox (badness 10000) in paragraph at lines 113--115 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Node.Node at- Underfull \hbox (badness 7291) in paragraph at lines 115--117 []\T1/pcr/m/n/10 DefaultSusceptibilityDistribution() \T1/ptm/m/n/10 (\T1/ptm/m/ it/10 in Overfull \hbox (46.96086pt too wide) in paragraph at lines 115--117 \T1/ptm/m/it/10 mod-ule emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/ 10 ), Underfull \hbox (badness 10000) in paragraph at lines 117--119 []\T1/pcr/m/n/10 DemographicsGenerator \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Overfull \hbox (17.1711pt too wide) in paragraph at lines 117--119 \T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 119--121 []\T1/pcr/m/n/10 DemographicsType \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Overfull \hbox (17.1711pt too wide) in paragraph at lines 119--121 \T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 121--123 []\T1/pcr/m/n/10 dtk_to_schema() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (56.83089pt too wide) in paragraph at lines 123--125 []\T1/pcr/m/n/10 dtk_version() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channel reports.channels.ChannelReport Overfull \hbox (25.71117pt too wide) in paragraph at lines 125--127 []\T1/pcr/m/n/10 dtk_version() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channel reports.channels.Header Underfull \hbox (badness 10000) in paragraph at lines 128--130 []\T1/pcr/m/n/10 DtkFile.Contents \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 130--132 []\T1/pcr/m/n/10 DtkFile.Objects \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 132--134 []\T1/pcr/m/n/10 DtkFileV1 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 134--136 []\T1/pcr/m/n/10 DtkFileV2 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 136--138 []\T1/pcr/m/n/10 DtkFileV2.NodesV2 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 138--140 []\T1/pcr/m/n/10 DtkFileV3 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 140--142 []\T1/pcr/m/n/10 DtkFileV3.NodesV3 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 142--144 []\T1/pcr/m/n/10 DtkFileV4 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 144--146 []\T1/pcr/m/n/10 DtkHeader \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 146--147 []\T1/pcr/m/n/10 dump_source() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 147--149 []\T1/pcr/m/n/10 dump_source() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 149--151 []\T1/pcr/m/n/10 dump_source() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 151--153 []\T1/pcr/m/n/10 duplicate_nodeID_check() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Overfull \hbox (46.65079pt too wide) in paragraph at lines 151--153 \T1/ptm/m/it/10 emod_api.demographics.DemographicsInputDataParsers\T1/ptm/m/n/1 0 ), Underfull \hbox (badness 10000) in paragraph at lines 156--158 []\T1/pcr/m/n/10 EllZeeFour \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Overfull \hbox (64.1225pt too wide) in paragraph at lines 170--171 []\T1/pcr/m/n/10 emod_api.config.default_from_schema_no_validation Overfull \hbox (34.1225pt too wide) in paragraph at lines 172--173 []\T1/pcr/m/n/10 emod_api.config.dtk_post_process_adhocevents [30] Overfull \hbox (28.1225pt too wide) in paragraph at lines 174--175 []\T1/pcr/m/n/10 emod_api.config.dtk_pre_process_adhocevents Overfull \hbox (28.1225pt too wide) in paragraph at lines 192--193 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsGenerator Overfull \hbox (70.1225pt too wide) in paragraph at lines 194--195 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsInputDataParsers Overfull \hbox (28.1225pt too wide) in paragraph at lines 196--197 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsTemplates Overfull \hbox (22.1225pt too wide) in paragraph at lines 204--205 []\T1/pcr/m/n/10 emod_api.examples.serialized_file_mc_to_sc Overfull \hbox (4.1225pt too wide) in paragraph at lines 224--225 []\T1/pcr/m/n/10 emod_api.schema.dtk_post_process_schema Overfull \hbox (28.1225pt too wide) in paragraph at lines 238--239 []\T1/pcr/m/n/10 emod_api.serialization.SerializedPopulation Overfull \hbox (16.1225pt too wide) in paragraph at lines 250--252 []\T1/pcr/m/n/10 EquilibriumAgeDistFromBirthAndMortRates() Overfull \hbox (59.97073pt too wide) in paragraph at lines 250--252 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule emod_api.demographics.DemographicsTe mplates\T1/ptm/m/n/10 ), Overfull \hbox (15.62103pt too wide) in paragraph at lines 252--254 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 258--260 []\T1/pcr/m/n/10 fill_nodes_legacy() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (46.65079pt too wide) in paragraph at lines 258--260 \T1/ptm/m/it/10 emod_api.demographics.DemographicsInputDataParsers\T1/ptm/m/n/1 0 ), Overfull \hbox (4.62106pt too wide) in paragraph at lines 260--262 []\T1/pcr/m/n/10 finalize() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.schema_to_ class.ReadOnlyDict Overfull \hbox (36.30013pt too wide) in paragraph at lines 262--264 []\T1/pcr/m/n/10 find() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule emod_api.ser ialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 264--266 []\T1/pcr/m/n/10 flattenConfig() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (81.59949pt too wide) in paragraph at lines 266--268 []\T1/pcr/m/n/10 flush() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization .SerializedPopulation.SerializedPopulation Underfull \hbox (badness 10000) in paragraph at lines 270--272 []\T1/pcr/m/n/10 from_data() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demograph ics.Node.Node Underfull \hbox (badness 10000) in paragraph at lines 272--274 []\T1/pcr/m/n/10 from_dataframe() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (17.1711pt too wide) in paragraph at lines 272--274 \T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 274--276 []\T1/pcr/m/n/10 from_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.w eather.Metadata Underfull \hbox (badness 10000) in paragraph at lines 276--278 []\T1/pcr/m/n/10 from_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 278--280 []\T1/pcr/m/n/10 from_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (17.1711pt too wide) in paragraph at lines 278--280 \T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 ), [31] Underfull \hbox (badness 10000) in paragraph at lines 280--282 []\T1/pcr/m/n/10 FullRisk() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 280--282 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 285--287 []\T1/pcr/m/n/10 generate_demographics() Overfull \hbox (115.97037pt too wide) in paragraph at lines 285--287 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator.Dem ographicsGenerator Underfull \hbox (badness 10000) in paragraph at lines 287--289 []\T1/pcr/m/n/10 generate_metadata() Overfull \hbox (115.97037pt too wide) in paragraph at lines 287--289 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator.Dem ographicsGenerator Overfull \hbox (173.87039pt too wide) in paragraph at lines 289--291 []\T1/pcr/m/n/10 generate_nodes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demo graphics.DemographicsGenerator.DemographicsGenerator Underfull \hbox (badness 10000) in paragraph at lines 291--293 []\T1/pcr/m/n/10 generatePopulation() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e Underfull \hbox (badness 10000) in paragraph at lines 291--293 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 293--295 []\T1/pcr/m/n/10 get_class_with_defaults() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in m od-ule Underfull \hbox (badness 10000) in paragraph at lines 295--297 []\T1/pcr/m/n/10 get_default_campaign_event() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 i n mod-ule Underfull \hbox (badness 10000) in paragraph at lines 297--299 []\T1/pcr/m/n/10 get_node_ids_from_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Overfull \hbox (105.59949pt too wide) in paragraph at lines 299--301 []\T1/pcr/m/n/10 get_nodes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializa tion.SerializedPopulation.SerializedPopulation Underfull \hbox (badness 10000) in paragraph at lines 301--303 []\T1/pcr/m/n/10 get_xpix_ypix() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 303--305 []\T1/pcr/m/n/10 getAttributeValues() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e Underfull \hbox (badness 10000) in paragraph at lines 303--305 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 305--307 []\T1/pcr/m/n/10 getIndividualsWithProperty() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 i n mod-ule Underfull \hbox (badness 10000) in paragraph at lines 305--307 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 307--309 []\T1/pcr/m/n/10 getNextIndividualSuid() Overfull \hbox (77.69946pt too wide) in paragraph at lines 307--309 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation.Ser ializedPopulation Underfull \hbox (badness 10000) in paragraph at lines 309--311 []\T1/pcr/m/n/10 getNextInfectionSuid() Overfull \hbox (77.69946pt too wide) in paragraph at lines 309--311 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation.Ser ializedPopulation Underfull \hbox (badness 10000) in paragraph at lines 311--313 []\T1/pcr/m/n/10 getPropertyValues2() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e Underfull \hbox (badness 10000) in paragraph at lines 311--313 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Overfull \hbox (26.83089pt too wide) in paragraph at lines 317--319 []\T1/pcr/m/n/10 header() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelrepor ts.channels.ChannelReport Underfull \hbox (badness 10000) in paragraph at lines 327--329 []\T1/pcr/m/n/10 id() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.spatialreports.s patial.SpatialNode Underfull \hbox (badness 7308) in paragraph at lines 329--330 []\T1/pcr/m/n/10 id() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.weather. WeatherNode prop- Overfull \hbox (6.84114pt too wide) in paragraph at lines 330--332 []\T1/pcr/m/n/10 id_reference() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weathe r.weather.Metadata Overfull \hbox (1.47115pt too wide) in paragraph at lines 332--334 []\T1/pcr/m/n/10 id_reference() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weathe r.weather.Weather Underfull \hbox (badness 10000) in paragraph at lines 334--336 []\T1/pcr/m/n/10 init_resolution_from_file() Underfull \hbox (badness 10000) in paragraph at lines 334--336 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Node.Node class Underfull \hbox (badness 10000) in paragraph at lines 336--338 []\T1/pcr/m/n/10 InitAgeUniform() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 336--338 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 338--340 []\T1/pcr/m/n/10 InitPrevUniform() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 338--340 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 340--342 []\T1/pcr/m/n/10 InitRiskUniform() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 340--342 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 342--344 []\T1/pcr/m/n/10 InitSusceptConstant() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le Overfull \hbox (15.62103pt too wide) in paragraph at lines 342--344 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 348--350 []\T1/pcr/m/n/10 lat_lon_from_nodeid() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le Underfull \hbox (badness 10000) in paragraph at lines 350--352 []\T1/pcr/m/n/10 load_default_config_as_rod() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 i n mod-ule Overfull \hbox (31.30106pt too wide) in paragraph at lines 350--352 \T1/ptm/m/it/10 emod_api.config.default_from_schema_no_validation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 352--354 []\T1/pcr/m/n/10 loadInfection() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 352--354 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 360--362 []\T1/pcr/m/n/10 make_config_from_poi() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule Underfull \hbox (badness 10000) in paragraph at lines 360--362 \T1/ptm/m/it/10 emod_api.config.from_poi_and_binary\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 362--364 []\T1/pcr/m/n/10 make_config_from_poi_and_config_dict() Overfull \hbox (16.3614pt too wide) in paragraph at lines 362--364 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule emod_api.config.from_poi_and_binary\ T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 364--366 []\T1/pcr/m/n/10 make_config_from_poi_and_config_file() Overfull \hbox (16.3614pt too wide) in paragraph at lines 364--366 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule emod_api.config.from_poi_and_binary\ T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 366--368 []\T1/pcr/m/n/10 make_config_from_poi_and_schema() \T1/ptm/m/n/10 (\T1/ptm/m/it /10 in Overfull \hbox (3.35153pt too wide) in paragraph at lines 366--368 \T1/ptm/m/it/10 mod-ule emod_api.config.from_poi_and_binary\T1/ptm/m/n/10 ), [32] Underfull \hbox (badness 10000) in paragraph at lines 369--370 []\T1/pcr/m/n/10 metadata() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.we ather.Weather Underfull \hbox (badness 10000) in paragraph at lines 370--371 []\T1/pcr/m/n/10 MigrationFile \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Overfull \hbox (2.6225pt too wide) in paragraph at lines 377--378 []| \T1/pcr/m/n/10 emod_api.config.default_from_schema\T1/ptm/m/n/10 , Overfull \hbox (86.6225pt too wide) in paragraph at lines 378--379 []| \T1/pcr/m/n/10 emod_api.config.default_from_schema_no_validation\T1/ptm/m/n /10 , Overfull \hbox (56.6225pt too wide) in paragraph at lines 379--380 []| \T1/pcr/m/n/10 emod_api.config.dtk_post_process_adhocevents\T1/ptm/m/n/10 , Overfull \hbox (50.6225pt too wide) in paragraph at lines 380--381 []| \T1/pcr/m/n/10 emod_api.config.dtk_pre_process_adhocevents\T1/ptm/m/n/10 , Overfull \hbox (8.6225pt too wide) in paragraph at lines 381--382 []| \T1/pcr/m/n/10 emod_api.config.dtk_pre_process_w5ml\T1/ptm/m/n/10 , Overfull \hbox (2.6225pt too wide) in paragraph at lines 383--384 []| \T1/pcr/m/n/10 emod_api.config.from_poi_and_binary\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 387--388 []| \T1/pcr/m/n/10 emod_api.demographics.demographics\T1/ptm/m/n/10 , Overfull \hbox (20.6225pt too wide) in paragraph at lines 388--389 []| \T1/pcr/m/n/10 emod_api.demographics.DemographicsFile\T1/ptm/m/n/10 , Overfull \hbox (50.6225pt too wide) in paragraph at lines 389--390 []| \T1/pcr/m/n/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 , Overfull \hbox (92.6225pt too wide) in paragraph at lines 390--391 []| \T1/pcr/m/n/10 emod_api.demographics.DemographicsInputDataParsers\T1/ptm/m/ n/10 , Overfull \hbox (50.6225pt too wide) in paragraph at lines 391--392 []| \T1/pcr/m/n/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 , Overfull \hbox (44.6225pt too wide) in paragraph at lines 395--396 []| \T1/pcr/m/n/10 emod_api.examples.serialized_file_mc_to_sc\T1/ptm/m/n/10 , Overfull \hbox (20.6225pt too wide) in paragraph at lines 399--400 []| \T1/pcr/m/n/10 emod_api.interventions.import_pressure\T1/ptm/m/n/10 , Overfull \hbox (14.6225pt too wide) in paragraph at lines 401--402 []| \T1/pcr/m/n/10 emod_api.interventions.simple_vaccine\T1/ptm/m/n/10 , Overfull \hbox (26.6225pt too wide) in paragraph at lines 405--406 []| \T1/pcr/m/n/10 emod_api.schema.dtk_post_process_schema\T1/ptm/m/n/10 , Overfull \hbox (14.6225pt too wide) in paragraph at lines 409--410 []| \T1/pcr/m/n/10 emod_api.serialization.dtkFileSupport\T1/ptm/m/n/10 , Overfull \hbox (2.6225pt too wide) in paragraph at lines 410--411 []| \T1/pcr/m/n/10 emod_api.serialization.dtkFileTools\T1/ptm/m/n/10 , Overfull \hbox (14.6225pt too wide) in paragraph at lines 411--412 []| \T1/pcr/m/n/10 emod_api.serialization.dtkFileUtility\T1/ptm/m/n/10 , Overfull \hbox (50.6225pt too wide) in paragraph at lines 412--413 []| \T1/pcr/m/n/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 418--420 []\T1/pcr/m/n/10 MortalityRateByAge() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e Overfull \hbox (15.62103pt too wide) in paragraph at lines 418--420 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Overfull \hbox (15.62103pt too wide) in paragraph at lines 420--422 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 425--427 []\T1/pcr/m/n/10 new_intervention() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 425--427 \T1/ptm/m/it/10 emod_api.interventions.import_pressure\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 427--429 []\T1/pcr/m/n/10 new_intervention() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 429--431 []\T1/pcr/m/n/10 new_intervention() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 429--431 \T1/ptm/m/it/10 emod_api.interventions.simple_vaccine\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 431--433 []\T1/pcr/m/n/10 new_intervention_as_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 433--435 []\T1/pcr/m/n/10 new_intervention_as_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 435--437 []\T1/pcr/m/n/10 new_intervention_as_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (32.8303pt too wide) in paragraph at lines 438--440 []\T1/pcr/m/n/10 node_count() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.spatialr eports.spatial.SpatialReport Underfull \hbox (badness 10000) in paragraph at lines 442--444 []\T1/pcr/m/n/10 node_count() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather. weather.Weather Underfull \hbox (badness 10000) in paragraph at lines 444--446 []\T1/pcr/m/n/10 node_ID_from_lat_long() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod -ule Overfull \hbox (46.65079pt too wide) in paragraph at lines 444--446 \T1/ptm/m/it/10 emod_api.demographics.DemographicsInputDataParsers\T1/ptm/m/n/1 0 ), Overfull \hbox (20.8303pt too wide) in paragraph at lines 446--448 []\T1/pcr/m/n/10 node_ids() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.spatialrep orts.spatial.SpatialReport Underfull \hbox (badness 10000) in paragraph at lines 448--450 []\T1/pcr/m/n/10 node_ids() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.we ather.Metadata Underfull \hbox (badness 10000) in paragraph at lines 450--451 []\T1/pcr/m/n/10 node_ids() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.we ather.Weather [33] Underfull \hbox (badness 10000) in paragraph at lines 451--453 []\T1/pcr/m/n/10 nodeid_from_lat_lon() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le Underfull \hbox (badness 5802) in paragraph at lines 453--455 []\T1/pcr/m/n/10 nodes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization .dtkFileTools.DtkFile Overfull \hbox (81.59949pt too wide) in paragraph at lines 455--457 []\T1/pcr/m/n/10 nodes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization .SerializedPopulation.SerializedPopulation Overfull \hbox (2.8303pt too wide) in paragraph at lines 457--459 []\T1/pcr/m/n/10 nodes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.spatialreport s.spatial.SpatialReport Underfull \hbox (badness 10000) in paragraph at lines 460--461 []\T1/pcr/m/n/10 nodes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.weath er.Weather prop- Underfull \hbox (badness 10000) in paragraph at lines 461--463 []\T1/pcr/m/n/10 nodes_for_DTK() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 463--465 []\T1/pcr/m/n/10 NoInitialPrevalence() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le Overfull \hbox (15.62103pt too wide) in paragraph at lines 463--465 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 465--467 []\T1/pcr/m/n/10 NoMigrationHeterogeneity() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 465--467 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 467--469 []\T1/pcr/m/n/10 NoRisk() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 467--469 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Overfull \hbox (62.83089pt too wide) in paragraph at lines 469--471 []\T1/pcr/m/n/10 num_channels() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channe lreports.channels.ChannelReport Overfull \hbox (31.71117pt too wide) in paragraph at lines 471--473 []\T1/pcr/m/n/10 num_channels() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channe lreports.channels.Header Overfull \hbox (74.83089pt too wide) in paragraph at lines 473--475 []\T1/pcr/m/n/10 num_time_steps() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.chan nelreports.channels.ChannelReport Overfull \hbox (43.71117pt too wide) in paragraph at lines 475--477 []\T1/pcr/m/n/10 num_time_steps() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.chan nelreports.channels.Header Underfull \hbox (badness 10000) in paragraph at lines 480--482 []\T1/pcr/m/n/10 printParameters() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 480--482 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 484--486 []\T1/pcr/m/n/10 provenance() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather. weather.Weather Overfull \hbox (1.84042pt too wide) in paragraph at lines 491--492 []\T1/pcr/m/n/10 read() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule emod_api.ser ialization.dtkFileTools\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 493--495 []\T1/pcr/m/n/10 recurser() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 493--495 \T1/ptm/m/it/10 emod_api.schema.dtk_post_process_schema\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 495--497 []\T1/pcr/m/n/10 removeIndividuals() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 495--497 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 497--499 []\T1/pcr/m/n/10 removeNumberIndividuals() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in m od-ule Underfull \hbox (badness 10000) in paragraph at lines 497--499 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Overfull \hbox (56.83089pt too wide) in paragraph at lines 499--501 []\T1/pcr/m/n/10 report_type() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channel reports.channels.ChannelReport Overfull \hbox (25.71117pt too wide) in paragraph at lines 501--503 []\T1/pcr/m/n/10 report_type() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channel reports.channels.Header Overfull \hbox (74.83089pt too wide) in paragraph at lines 503--505 []\T1/pcr/m/n/10 report_version() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.chan nelreports.channels.ChannelReport Overfull \hbox (43.71117pt too wide) in paragraph at lines 505--507 []\T1/pcr/m/n/10 report_version() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.chan nelreports.channels.Header Overfull \hbox (4.77174pt too wide) in paragraph at lines 507--509 []\T1/pcr/m/n/10 res_in_degrees \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demogr aphics.Node.Node Underfull \hbox (badness 10000) in paragraph at lines 513--515 []\T1/pcr/m/n/10 SchemaConfigBuilder \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 515--517 []\T1/pcr/m/n/10 SchemaConfigBuilder \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 517--519 []\T1/pcr/m/n/10 serialized_dtk_to_json() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 517--519 \T1/ptm/m/it/10 emod_api.examples.serialized_file_mc_to_sc\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 519--521 []\T1/pcr/m/n/10 SerializedPopulation \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 519--521 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 521--523 []\T1/pcr/m/n/10 SerialObject \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 523--525 []\T1/pcr/m/n/10 set_demog_distributions() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in m od-ule Underfull \hbox (badness 10000) in paragraph at lines 523--525 \T1/ptm/m/it/10 emod_api.demographics.demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 525--527 []\T1/pcr/m/n/10 set_growing_demographics() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 527--529 []\T1/pcr/m/n/10 set_immune_mod() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 527--529 \T1/ptm/m/it/10 emod_api.demographics.demographics\T1/ptm/m/n/10 ), Overfull \hbox (173.87039pt too wide) in paragraph at lines 529--531 []\T1/pcr/m/n/10 set_resolution() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demo graphics.DemographicsGenerator.DemographicsGenerator Underfull \hbox (badness 10000) in paragraph at lines 531--533 []\T1/pcr/m/n/10 set_risk_mod() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 531--533 \T1/ptm/m/it/10 emod_api.demographics.demographics\T1/ptm/m/n/10 ), Overfull \hbox (16.62106pt too wide) in paragraph at lines 533--535 []\T1/pcr/m/n/10 set_schema() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.schema_t o_class.ReadOnlyDict Underfull \hbox (badness 10000) in paragraph at lines 535--537 []\T1/pcr/m/n/10 set_schema() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 535--537 \T1/ptm/m/it/10 emod_api.config.from_poi_and_binary\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 537--539 []\T1/pcr/m/n/10 set_static_demographics() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in m od-ule Underfull \hbox (badness 10000) in paragraph at lines 537--539 \T1/ptm/m/it/10 emod_api.demographics.demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 539--541 []\T1/pcr/m/n/10 setAttribute() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 539--541 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), [34] Underfull \hbox (badness 10000) in paragraph at lines 541--543 []\T1/pcr/m/n/10 setAttributes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 541--543 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 543--545 []\T1/pcr/m/n/10 setIndividualPropertyInfections() \T1/ptm/m/n/10 (\T1/ptm/m/it /10 in Overfull \hbox (25.39023pt too wide) in paragraph at lines 543--545 \T1/ptm/m/it/10 mod-ule 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configjson_path\T1/ptm/m/n/10 , Overfull \hbox (63.52425pt too wide) in paragraph at lines 442--442 []\T1/ptm/m/it/10 start_config_dict\T1/ptm/m/n/10 , Overfull \hbox (71.87448pt too wide) in paragraph at lines 442--442 \T1/ptm/m/it/10 poi_set_param_fn\T1/pcr/m/n/10 ) Overfull \hbox (66.30441pt too wide) in paragraph at lines 451--451 []\T1/ptm/m/it/10 start_config_path\T1/ptm/m/n/10 , Overfull \hbox (71.87448pt too wide) in paragraph at lines 451--451 \T1/ptm/m/it/10 poi_set_param_fn\T1/pcr/m/n/10 ) Overfull \hbox (18.36475pt too wide) in paragraph at lines 460--460 []\T1/ptm/m/it/10 schema_path\T1/ptm/m/n/10 , Overfull \hbox (41.87448pt too wide) in paragraph at lines 460--460 \T1/ptm/m/it/10 poi_set_param_fn\T1/pcr/m/n/10 ) [5] Underfull \hbox (badness 10000) in paragraph at lines 469--469 []\T1/ptm/m/it/10 eradication_path\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 517--519 []\T1/ptm/m/n/10 builder = s2c.SchemaConfigBuilder( Underfull \hbox (badness 10000) in paragraph at lines 526--526 []\T1/ptm/m/it/10 schema_name=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 schema.json\TS1 /ptm/m/it/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 526--526 \T1/ptm/m/it/10 model=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 GENERIC_SIM\TS1/ptm/m/i t/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 526--526 \T1/ptm/m/it/10 con-fig_out=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 config.json\TS1/p tm/m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (28.28418pt too wide) in paragraph at lines 537--537 []\T1/ptm/m/it/10 schema_name=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 schema.json\TS1 /ptm/m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (11.09424pt too wide) in paragraph at lines 537--537 \T1/ptm/m/it/10 model=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 GENERIC_SIM\TS1/ptm/m/i t/10 '\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 537--537 \T1/ptm/m/it/10 con- Underfull \hbox (badness 10000) in paragraph at lines 537--537 \T1/ptm/m/it/10 fig_out=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 config.json\TS1/ptm/m /it/10 '\T1/ptm/m/n/10 , [6] Overfull \hbox (6.87448pt too wide) in paragraph at lines 566--566 []\T1/ptm/m/it/10 demographics_file\T1/pcr/m/n/10 ) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) Overfull \hbox (18.60422pt too wide) in paragraph at lines 615--615 []\T1/ptm/m/it/10 res_in_arcsec\T1/pcr/m/n/10 ) Overfull \hbox (13.07484pt too wide) in paragraph at lines 634--634 []\T1/ptm/m/it/10 nodes\T1/ptm/m/n/10 , Overfull \hbox (5.01491pt too wide) in paragraph at lines 634--634 \T1/ptm/m/it/10 con- Overfull \hbox (12.23463pt too wide) in paragraph at lines 634--634 \T1/ptm/m/it/10 cerns: Overfull \hbox (2.79494pt too wide) in paragraph at lines 634--634 \T1/ptm/m/it/10 Op- Overfull \hbox (457.54115pt too wide) in paragraph at lines 634--634 \T1/ptm/m/it/10 tional[Union[emod_api.dtk_tools.demographics.DemographicsGenera torConcern.DemographicsGeneratorConcern, Overfull \hbox (429.49101pt too wide) in paragraph at lines 634--634 \T1/ptm/m/it/10 List[emod_api.dtk_tools.demographics.DemographicsGeneratorConce rn.DemographicsGeneratorConcern]]] Underfull \hbox (badness 10000) in paragraph at lines 634--634 \T1/ptm/m/it/10 = Overfull \hbox (10.85487pt too wide) in paragraph at lines 634--634 \T1/ptm/m/it/10 None\T1/ptm/m/n/10 , Overfull \hbox (84.4637pt too wide) in paragraph at lines 634--634 \T1/ptm/m/it/10 res_in_arcsec=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 custom\TS1/ptm/ m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (115.46402pt too wide) in paragraph at lines 634--634 \T1/ptm/m/it/10 node_id_from_lat_long=False\T1/pcr/m/n/10 ) [7] Underfull \hbox (badness 10000) in paragraph at lines 746--746 []\T1/ptm/m/it/10 df\T1/ptm/m/n/10 , \T1/ptm/m/it/10 de-mo-graph- Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 ics_filename: Op- Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 tional[str] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 con-cerns: Op- Overfull \hbox (379.54115pt too wide) in paragraph at lines 746--746 \T1/ptm/m/it/10 tional[Union[emod_api.dtk_tools.demographics.DemographicsGenera torConcern.DemographicsGeneratorConcern, Overfull \hbox (351.49101pt too wide) in paragraph at lines 746--746 \T1/ptm/m/it/10 List[emod_api.dtk_tools.demographics.DemographicsGeneratorConce rn.DemographicsGeneratorConcern]]] Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Overfull \hbox (6.4637pt too wide) in paragraph at lines 746--746 \T1/ptm/m/it/10 res_in_arcsec=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 custom\TS1/ptm/ m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (30.83415pt too wide) in paragraph at lines 746--746 \T1/ptm/m/it/10 node_id_from_lat_long=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 de-fault_population: Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 int = 1000\T1/ptm/m/n/10 , Overfull \hbox (79.21327pt too wide) in paragraph at lines 746--746 \T1/ptm/m/it/10 load_other_columns_as_attributes=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 tional[List[str]] Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ex- Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 clude_columns: Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 Op-tional[List[str]] Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Overfull \hbox (0.89452pt too wide) in paragraph at lines 746--746 \T1/ptm/m/it/10 nodeid_column_name: Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 Op-tional[str] Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lat-i- Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 str = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 lat\TS1/ptm/m/it/10 '\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 lon-gi- Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 746--746 \T1/ptm/m/it/10 tion_column_name: [8] Overfull \hbox (54.94496pt too wide) in paragraph at lines 761--762 []\T1/pcr/b/n/10 apply. If not specified, we use the DefaultWorldBankEquilibriu mConcern [9] Underfull \hbox (badness 10000) in paragraph at lines 809--809 []\T1/ptm/m/it/10 population_input_file: Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 str\T1/ptm/m/n/10 , \T1/ptm/m/it/10 de-mo-graph- Underfull \hbox (badness 7851) in paragraph at lines 809--809 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 con-cerns: Op- Overfull \hbox (349.54115pt too wide) in paragraph at lines 809--809 \T1/ptm/m/it/10 tional[Union[emod_api.dtk_tools.demographics.DemographicsGenera torConcern.DemographicsGeneratorConcern, Overfull \hbox (321.49101pt too wide) in paragraph at lines 809--809 \T1/ptm/m/it/10 List[emod_api.dtk_tools.demographics.DemographicsGeneratorConce rn.DemographicsGeneratorConcern]]] Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 res_in_arcsec=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 custom\TS1/ptm/ m/it/10 '\T1/ptm/m/n/10 , Overfull \hbox (0.83415pt too wide) in paragraph at lines 809--809 \T1/ptm/m/it/10 node_id_from_lat_long=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 de-fault_population: Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 int = 1000\T1/ptm/m/n/10 , Overfull \hbox (49.21327pt too wide) in paragraph at lines 809--809 \T1/ptm/m/it/10 load_other_columns_as_attributes=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 in-clude_columns: Op- Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 tional[List[str]] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 ex-clude_columns: Op- Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 tional[List[str]] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 nodeid_column_name: Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 Op-tional[str] = None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 lat-i-tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 str = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 lat\TS1/ptm/m/it/10 '\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 lon-gi- Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 tude_column_name: Underfull \hbox (badness 10000) in paragraph at lines 809--809 \T1/ptm/m/it/10 str = \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 lon\TS1/ptm/m/it/10 '\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 pop-u-la- Underfull \hbox (badness 6236) in paragraph at lines 809--809 \T1/ptm/m/it/10 tion_column_name: str = Overfull \hbox (54.94496pt too wide) in paragraph at lines 824--825 []\T1/pcr/b/n/10 apply. If not specified, we use the DefaultWorldBankEquilibriu mConcern [10] Overfull \hbox (6.3048pt too wide) in paragraph at lines 880--880 []\T1/ptm/m/it/10 lat\T1/ptm/m/n/10 , Overfull \hbox (13.5249pt too wide) in paragraph at lines 880--880 \T1/ptm/m/it/10 long\T1/ptm/m/n/10 , Overfull \hbox (115.34473pt too wide) in paragraph at lines 880--880 \T1/ptm/m/it/10 res=0.008333333333333333\T1/pcr/m/n/10 ) Overfull \hbox (37.09444pt too wide) in paragraph at lines 886--886 []\T1/ptm/m/it/10 nodelist\T1/pcr/m/n/10 ) Overfull \hbox (11.74474pt too wide) in paragraph at lines 892--892 []\T1/ptm/m/it/10 node_info\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 892--892 \T1/ptm/m/it/10 De- Underfull \hbox (badness 10000) in paragraph at lines 892--892 \T1/ptm/m/it/10 moDf\T1/ptm/m/n/10 , Overfull \hbox (91.34473pt too wide) in paragraph at lines 892--892 \T1/ptm/m/it/10 res=0.008333333333333333\T1/pcr/m/n/10 ) Overfull \hbox (71.74474pt too wide) in paragraph at lines 898--898 []\T1/ptm/m/it/10 node_info\T1/ptm/m/n/10 , Overfull \hbox (41.2549pt too wide) in paragraph at lines 898--898 \T1/ptm/m/it/10 ex- Overfull \hbox (118.90427pt too wide) in paragraph at lines 898--898 \T1/ptm/m/it/10 tra_data_columns=[]\T1/ptm/m/n/10 , Overfull \hbox (151.34473pt too wide) in paragraph at lines 898--898 \T1/ptm/m/it/10 res=0.008333333333333333\T1/pcr/m/n/10 ) [11] Overfull \hbox (124.04425pt too wide) in paragraph at lines 949--949 []\T1/ptm/m/it/10 meanAgeAtInfection=2.5\T1/pcr/m/n/10 ) Overfull \hbox (29.24501pt too wide) in paragraph at lines 955--955 []\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 961--961 []\T1/ptm/m/it/10 AgeBins\T1/ptm/m/n/10 , \T1/ptm/m/it/10 Mor- Overfull \hbox (149.88425pt too wide) in paragraph at lines 993--993 []\T1/ptm/m/it/10 CrudeBirthRate=0.04\T1/ptm/m/n/10 , Overfull \hbox (87.57472pt too wide) in paragraph at lines 993--993 \T1/ptm/m/it/10 Crude- Overfull \hbox (79.59486pt too wide) in paragraph at lines 993--993 \T1/ptm/m/it/10 Mor- Overfull \hbox (110.60472pt too wide) in paragraph at lines 993--993 \T1/ptm/m/it/10 tRate=0.02\T1/pcr/m/n/10 ) Overfull \hbox (22.9045pt too wide) in paragraph at lines 1074--1074 []\T1/ptm/m/it/10 nodeid\T1/ptm/m/n/10 , \T1/ptm/m/it/10 res_in_deg=0.041666666 666666664\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1080--1080 []\T1/ptm/m/it/10 lat\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lon\T1/ptm/m/n/10 , Overfull \hbox (9.16464pt too wide) in paragraph at lines 1080--1080 \T1/ptm/m/it/10 res_in_deg=0.041666666666666664\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1086--1086 []\T1/ptm/m/it/10 lat\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lon\T1/ptm/m/n/10 , [12] Underfull \hbox (badness 10000) in paragraph at lines 1115--1116 []\T1/pcr/b/n/10 distribution \T1/ptm/m/n/10 ^^U The se-lected dis-tri-bu-tion (need to come from Underfull \hbox (badness 10000) in paragraph at lines 1136--1137 \T1/ptm/m/n/10 Set the \T1/pcr/m/n/10 ImmunityDistributionFlag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ImmunityDistribution1 \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 1189--1189 []\T1/ptm/m/it/10 filename\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dis-tri-bu- [13] Underfull \hbox (badness 10000) in paragraph at lines 1233--1233 []\T1/ptm/m/it/10 cb\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1259--1259 []\T1/ptm/m/it/10 cb\T1/ptm/m/n/10 , [14] Overfull \hbox (19.2944pt too wide) in paragraph at lines 1309--1309 []\T1/ptm/m/it/10 filename_format\T1/ptm/m/n/10 , Overfull \hbox (3.61461pt too wide) in paragraph at lines 1309--1309 \T1/ptm/m/it/10 core_idx=0\T1/pcr/m/n/10 ) [15] Underfull \hbox (badness 10000) in paragraph at lines 1442--1442 []\T1/ptm/m/it/10 timestep\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file- [16] Overfull \hbox (24.70302pt too wide) in paragraph at lines 1519--1519 []\T1/ptm/m/it/10 path_to_binary\T1/ptm/m/n/10 , \T1/ptm/m/it/10 path_to_write_ schema=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 schema.json\TS1/ptm/m/it/10 '\T1/pcr/m /n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1603--1603 []\T1/ptm/m/it/10 node_id\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1603--1603 \T1/ptm/m/it/10 num- Overfull \hbox (9.63463pt too wide) in paragraph at lines 1603--1603 \T1/ptm/m/it/10 ber_of_ind\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1615--1615 []\T1/ptm/m/it/10 node_id\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1615--1615 \T1/ptm/m/it/10 num- Underfull \hbox (badness 10000) in paragraph at lines 1615--1615 \T1/ptm/m/it/10 ber_of_ind\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1615--1615 \T1/ptm/m/it/10 prop-er-ties\T1/ptm/m/n/10 , Overfull \hbox (45.96484pt too wide) in paragraph at lines 1621--1621 []\T1/ptm/m/it/10 node_id\T1/ptm/m/n/10 , Overfull \hbox (22.35486pt too wide) in paragraph at lines 1621--1621 \T1/ptm/m/it/10 in- Overfull \hbox (22.35486pt too wide) in paragraph at lines 1621--1621 \T1/ptm/m/it/10 di- Overfull \hbox (26.7948pt too wide) in paragraph at lines 1621--1621 \T1/ptm/m/it/10 vid- Overfull \hbox (43.74474pt too wide) in paragraph at lines 1621--1621 \T1/ptm/m/it/10 ual_idx\T1/ptm/m/n/10 , Overfull \hbox (58.84471pt too wide) in paragraph at lines 1621--1621 \T1/ptm/m/it/10 prop_value\T1/ptm/m/n/10 , Overfull \hbox (29.57497pt too wide) in paragraph at lines 1621--1621 \T1/ptm/m/it/10 han- Overfull \hbox (29.46484pt too wide) in paragraph at lines 1621--1621 \T1/ptm/m/it/10 dle\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1627--1627 []\T1/ptm/m/it/10 prop_values\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1627--1627 \T1/ptm/m/it/10 node\T1/ptm/m/n/10 , [17] Underfull \hbox (badness 10000) in paragraph at lines 1642--1642 []\T1/ptm/m/it/10 attribute\T1/ptm/m/n/10 , \T1/ptm/m/it/10 han-dle\T1/ptm/m/n/ 10 , \T1/ptm/m/it/10 fil- Underfull \hbox (badness 10000) in paragraph at lines 1642--1642 \T1/ptm/m/it/10 ter_fct=>\T1/pcr/m/n/10 ) Overfull \hbox (28.96484pt too wide) in paragraph at lines 1676--1676 []\T1/ptm/m/it/10 handle\T1/ptm/m/n/10 , Overfull \hbox (10.35486pt too wide) in paragraph at lines 1676--1676 \T1/ptm/m/it/10 in- Overfull \hbox (14.23474pt too wide) in paragraph at lines 1676--1676 \T1/ptm/m/it/10 fec- Overfull \hbox (17.3048pt too wide) in paragraph at lines 1676--1676 \T1/ptm/m/it/10 tion\T1/ptm/m/n/10 , Overfull \hbox (55.52435pt too wide) in paragraph at lines 1676--1676 \T1/ptm/m/it/10 fct=>\T1/pcr/m/n/10 ) Underfull \hbox (badness 10000) in paragraph at lines 1684--1684 []\T1/ptm/m/it/10 suid\T1/ptm/m/n/10 , \T1/ptm/m/it/10 kwargs={}\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1684--1684 \T1/ptm/m/it/10 copy_ind=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1704--1704 []\T1/ptm/m/it/10 name\T1/ptm/m/n/10 , \T1/ptm/m/it/10 han-dle\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cur- Underfull \hbox (badness 10000) in paragraph at lines 1710--1710 []\T1/ptm/m/it/10 handle\T1/ptm/m/n/10 , \T1/ptm/m/it/10 cur- Overfull \hbox (5.06378pt too wide) in paragraph at lines 1710--1710 \T1/ptm/m/it/10 rentlevel=\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 dtk.nodes\TS1/ptm/m /it/10 '\T1/pcr/m/n/10 ) [18] Underfull \hbox (badness 6493) in paragraph at lines 1808--1808 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 byte-count\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunkcount\TS1/ptm/m/it/10 '\T1/ptm/m/it/ 10 : Underfull \hbox (badness 10000) in paragraph at lines 1808--1808 \T1/ptm/m/it/10 0, \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 chunk-sizes\TS1/ptm/m/it/1 0 '\T1/ptm/m/it/10 : [], \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 com- Underfull \hbox (badness 6575) in paragraph at lines 1808--1808 \T1/ptm/m/it/10 10 17:20:59 2020\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 , \TS1/ptm/m/ it/10 '\T1/ptm/m/it/10 en-gine\TS1/ptm/m/it/10 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chunk-sizes\TS1/ptm/m/it/1 0 '\T1/ptm/m/it/10 : [], \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 com- Underfull \hbox (badness 6575) in paragraph at lines 1982--1982 \T1/ptm/m/it/10 10 17:20:59 2020\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 , \TS1/ptm/m/ it/10 '\T1/ptm/m/it/10 en-gine\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : Underfull \hbox (badness 10000) in paragraph at lines 1982--1982 \TS1/ptm/m/it/10 '\T1/ptm/m/it/10 ver-sion\TS1/ptm/m/it/10 '\T1/ptm/m/it/10 : 1 }\T1/ptm/m/n/10 , \T1/ptm/m/it/10 file-name=\TS1/ptm/m/it/10 ''\T1/ptm/m/n/10 , [20] [21] [22] [23] Underfull \hbox (badness 10000) in paragraph at lines 2389--2391 []\T1/ptm/m/n/10 python -m Underfull \hbox (badness 10000) in paragraph at lines 2392--2394 []\T1/ptm/m/n/10 python -m [24] Chapter 2. [25] [26] Overfull \hbox (66.6225pt too wide) in paragraph at lines 2444--2445 []\T1/pcr/m/n/10 emod_api.config.default_from_schema_no_validation\T1/ptm/m/n/1 0 , Overfull \hbox (36.6225pt too wide) in paragraph at lines 2445--2446 []\T1/pcr/m/n/10 emod_api.config.dtk_post_process_adhocevents\T1/ptm/m/n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 2446--2447 []\T1/pcr/m/n/10 emod_api.config.dtk_pre_process_adhocevents\T1/ptm/m/n/10 , Overfull \hbox (0.6225pt too wide) in paragraph at lines 2454--2455 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsFile\T1/ptm/m/n/10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 2455--2456 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 , Overfull \hbox (72.6225pt too wide) in paragraph at lines 2456--2457 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsInputDataParsers\T1/ptm/m/n/ 10 , Overfull \hbox (30.6225pt too wide) in paragraph at lines 2457--2458 []\T1/pcr/m/n/10 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emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 , [27] (./institute-for-disease-modeling-emod-api.ind [28] Overfull \hbox (30.30013pt too wide) in paragraph at lines 9--11 []\T1/pcr/m/n/10 add() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule emod_api.seri alization.SerializedPopulation\T1/ptm/m/n/10 ), Overfull \hbox (123.59949pt too wide) in paragraph at lines 11--13 []\T1/pcr/m/n/10 addInfection() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serial ization.SerializedPopulation.SerializedPopulation Overfull \hbox (8.17026pt too wide) in paragraph at lines 13--15 \T1/ptm/m/it/10 ule emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ) , Underfull \hbox (badness 10000) in paragraph at lines 15--17 []\T1/pcr/m/n/10 AgeStructureUNWPP() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 15--17 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Overfull \hbox (37.49991pt too wide) in paragraph at lines 17--19 []\T1/pcr/m/n/10 append() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializatio n.dtkFileTools.DtkFile.Contents Overfull \hbox (32.4899pt too wide) in paragraph at lines 19--21 []\T1/pcr/m/n/10 append() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializatio n.dtkFileTools.DtkFile.Objects Underfull \hbox (badness 10000) in paragraph at lines 21--23 []\T1/pcr/m/n/10 application() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (7.95116pt too wide) in paragraph at lines 21--23 \T1/ptm/m/it/10 emod_api.config.dtk_post_process_adhocevents\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 23--25 []\T1/pcr/m/n/10 application() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (4.2412pt too wide) in paragraph at lines 23--25 \T1/ptm/m/it/10 emod_api.config.dtk_pre_process_adhocevents\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 25--27 []\T1/pcr/m/n/10 application() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 25--27 \T1/ptm/m/it/10 emod_api.config.dtk_pre_process_w5ml\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 27--29 []\T1/pcr/m/n/10 application() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 27--29 \T1/ptm/m/it/10 emod_api.schema.dtk_post_process_schema\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 29--31 []\T1/pcr/m/n/10 apply_to_defaults_or_nodes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 i n mod-ule Underfull \hbox (badness 10000) in paragraph at lines 31--33 []\T1/pcr/m/n/10 arcsec_to_deg() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (17.1711pt too wide) in paragraph at lines 31--33 \T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 ), Overfull \hbox (62.83089pt too wide) in paragraph at lines 33--35 []\T1/pcr/m/n/10 as_dataframe() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channe lreports.channels.ChannelReport Overfull \hbox (41.61118pt too wide) in paragraph at lines 35--37 []\T1/pcr/m/n/10 as_dictionary() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.chann elreports.channels.Channel Overfull \hbox (37.71117pt too wide) in paragraph at lines 37--39 []\T1/pcr/m/n/10 as_dictionary() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.chann elreports.channels.Header Underfull \hbox (badness 10000) in paragraph at lines 48--49 []\T1/pcr/m/n/10 basicNode() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (23.59027pt too wide) in paragraph at lines 50--52 []\T1/pcr/m/n/10 byte_count() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializ ation.dtkFileTools.DtkFile Underfull \hbox (badness 10000) in paragraph at lines 55--57 []\T1/pcr/m/n/10 changeSusceptibility() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule Underfull \hbox (badness 10000) in paragraph at lines 55--57 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Overfull \hbox (68.83089pt too wide) in paragraph at lines 58--60 []\T1/pcr/m/n/10 channel_names() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.chann elreports.channels.ChannelReport Underfull \hbox (badness 10000) in paragraph at lines 60--62 []\T1/pcr/m/n/10 ChannelReport \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Overfull \hbox (38.83089pt too wide) in paragraph at lines 62--64 []\T1/pcr/m/n/10 channels() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelrep orts.channels.ChannelReport Overfull \hbox (29.59027pt too wide) in paragraph at lines 64--66 []\T1/pcr/m/n/10 chunk_count() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.seriali zation.dtkFileTools.DtkFile Overfull \hbox (29.59027pt too wide) in paragraph at lines 66--68 []\T1/pcr/m/n/10 chunk_sizes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.seriali zation.dtkFileTools.DtkFile Overfull \hbox (36.91025pt too wide) in paragraph at lines 70--72 []\T1/pcr/m/n/10 compress() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializat ion.dtkFileSupport.EllZeeFour Overfull \hbox (21.29066pt too wide) in paragraph at lines 72--74 []\T1/pcr/m/n/10 compress() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializat ion.dtkFileSupport.Snappy Overfull \hbox (50.91016pt too wide) in paragraph at lines 74--76 []\T1/pcr/m/n/10 compress() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializat ion.dtkFileSupport.Uncompressed Underfull \hbox (badness 10000) in paragraph at lines 76--78 []\T1/pcr/m/n/10 compress() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (23.59027pt too wide) in paragraph at lines 78--80 []\T1/pcr/m/n/10 compressed() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializ ation.dtkFileTools.DtkFile Overfull \hbox (29.59027pt too wide) in paragraph at lines 80--82 []\T1/pcr/m/n/10 compression() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.seriali zation.dtkFileTools.DtkFile [29] Underfull \hbox (badness 10000) in paragraph at lines 82--84 []\T1/pcr/m/n/10 ConstantMortality() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 82--84 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Overfull \hbox (46.65079pt too wide) in paragraph at lines 84--86 \T1/ptm/m/it/10 emod_api.demographics.DemographicsInputDataParsers\T1/ptm/m/n/1 0 ), Underfull \hbox (badness 10000) in paragraph at lines 86--87 []\T1/pcr/m/n/10 Coordinate \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 87--89 []\T1/pcr/m/n/10 createIndividual() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 87--89 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Overfull \hbox (12.84114pt too wide) in paragraph at lines 89--91 []\T1/pcr/m/n/10 creation_date() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weath er.weather.Metadata Overfull \hbox (7.47115pt too wide) in paragraph at lines 91--93 []\T1/pcr/m/n/10 creation_date() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weath er.weather.Weather Underfull \hbox (badness 10000) in paragraph at lines 96--98 []\T1/pcr/m/n/10 data() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelreports .channels.Channel Underfull \hbox (badness 10000) in paragraph at lines 98--100 []\T1/pcr/m/n/10 data() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.spatialreports .spatial.SpatialNode Underfull \hbox (badness 10000) in paragraph at lines 104--106 []\T1/pcr/m/n/10 datavalue_count() Underfull \hbox (badness 10000) in paragraph at lines 104--106 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.weather.Metadata prop- Underfull \hbox (badness 10000) in paragraph at lines 106--108 []\T1/pcr/m/n/10 datavalue_count() Underfull \hbox (badness 10000) in paragraph at lines 106--108 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.weather.Weather prop- Underfull \hbox (badness 10000) in paragraph at lines 108--110 []\T1/pcr/m/n/10 date() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization. dtkFileTools.DtkFile Underfull \hbox (badness 10000) in paragraph at lines 110--111 []\T1/pcr/m/n/10 decode() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (10.77174pt too wide) in paragraph at lines 111--113 []\T1/pcr/m/n/10 default_density \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demog raphics.Node.Node Underfull \hbox (badness 10000) in paragraph at lines 113--115 []\T1/pcr/m/n/10 default_population Underfull \hbox (badness 10000) in paragraph at lines 113--115 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Node.Node at- Underfull \hbox (badness 7291) in paragraph at lines 115--117 []\T1/pcr/m/n/10 DefaultSusceptibilityDistribution() \T1/ptm/m/n/10 (\T1/ptm/m/ it/10 in Overfull \hbox (46.96086pt too wide) in paragraph at lines 115--117 \T1/ptm/m/it/10 mod-ule emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/ 10 ), Underfull \hbox (badness 10000) in paragraph at lines 117--119 []\T1/pcr/m/n/10 DemographicsGenerator \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Overfull \hbox (17.1711pt too wide) in paragraph at lines 117--119 \T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 119--121 []\T1/pcr/m/n/10 DemographicsType \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Overfull \hbox (17.1711pt too wide) in paragraph at lines 119--121 \T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 121--123 []\T1/pcr/m/n/10 dtk_to_schema() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (56.83089pt too wide) in paragraph at lines 123--125 []\T1/pcr/m/n/10 dtk_version() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channel reports.channels.ChannelReport Overfull \hbox (25.71117pt too wide) in paragraph at lines 125--127 []\T1/pcr/m/n/10 dtk_version() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channel reports.channels.Header Underfull \hbox (badness 10000) in paragraph at lines 128--130 []\T1/pcr/m/n/10 DtkFile.Contents \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 130--132 []\T1/pcr/m/n/10 DtkFile.Objects \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 132--134 []\T1/pcr/m/n/10 DtkFileV1 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 134--136 []\T1/pcr/m/n/10 DtkFileV2 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 136--138 []\T1/pcr/m/n/10 DtkFileV2.NodesV2 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 138--140 []\T1/pcr/m/n/10 DtkFileV3 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 140--142 []\T1/pcr/m/n/10 DtkFileV3.NodesV3 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 142--144 []\T1/pcr/m/n/10 DtkFileV4 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 144--146 []\T1/pcr/m/n/10 DtkHeader \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 146--147 []\T1/pcr/m/n/10 dump_source() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 147--149 []\T1/pcr/m/n/10 dump_source() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 149--151 []\T1/pcr/m/n/10 dump_source() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 151--153 []\T1/pcr/m/n/10 duplicate_nodeID_check() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Overfull \hbox (46.65079pt too wide) in paragraph at lines 151--153 \T1/ptm/m/it/10 emod_api.demographics.DemographicsInputDataParsers\T1/ptm/m/n/1 0 ), Underfull \hbox (badness 10000) in paragraph at lines 156--158 []\T1/pcr/m/n/10 EllZeeFour \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Overfull \hbox (64.1225pt too wide) in paragraph at lines 170--171 []\T1/pcr/m/n/10 emod_api.config.default_from_schema_no_validation Overfull \hbox (34.1225pt too wide) in paragraph at lines 172--173 []\T1/pcr/m/n/10 emod_api.config.dtk_post_process_adhocevents [30] Overfull \hbox (28.1225pt too wide) in paragraph at lines 174--175 []\T1/pcr/m/n/10 emod_api.config.dtk_pre_process_adhocevents Overfull \hbox (28.1225pt too wide) in paragraph at lines 192--193 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsGenerator Overfull \hbox (70.1225pt too wide) in paragraph at lines 194--195 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsInputDataParsers Overfull \hbox (28.1225pt too wide) in paragraph at lines 196--197 []\T1/pcr/m/n/10 emod_api.demographics.DemographicsTemplates Overfull \hbox (22.1225pt too wide) in paragraph at lines 204--205 []\T1/pcr/m/n/10 emod_api.examples.serialized_file_mc_to_sc Overfull \hbox (4.1225pt too wide) in paragraph at lines 224--225 []\T1/pcr/m/n/10 emod_api.schema.dtk_post_process_schema Overfull \hbox (28.1225pt too wide) in paragraph at lines 238--239 []\T1/pcr/m/n/10 emod_api.serialization.SerializedPopulation Overfull \hbox (16.1225pt too wide) in paragraph at lines 250--252 []\T1/pcr/m/n/10 EquilibriumAgeDistFromBirthAndMortRates() Overfull \hbox (59.97073pt too wide) in paragraph at lines 250--252 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule emod_api.demographics.DemographicsTe mplates\T1/ptm/m/n/10 ), Overfull \hbox (15.62103pt too wide) in paragraph at lines 252--254 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 258--260 []\T1/pcr/m/n/10 fill_nodes_legacy() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (46.65079pt too wide) in paragraph at lines 258--260 \T1/ptm/m/it/10 emod_api.demographics.DemographicsInputDataParsers\T1/ptm/m/n/1 0 ), Overfull \hbox (4.62106pt too wide) in paragraph at lines 260--262 []\T1/pcr/m/n/10 finalize() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.schema_to_ class.ReadOnlyDict Overfull \hbox (36.30013pt too wide) in paragraph at lines 262--264 []\T1/pcr/m/n/10 find() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule emod_api.ser ialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 264--266 []\T1/pcr/m/n/10 flattenConfig() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (81.59949pt too wide) in paragraph at lines 266--268 []\T1/pcr/m/n/10 flush() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization .SerializedPopulation.SerializedPopulation Underfull \hbox (badness 10000) in paragraph at lines 270--272 []\T1/pcr/m/n/10 from_data() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demograph ics.Node.Node Underfull \hbox (badness 10000) in paragraph at lines 272--274 []\T1/pcr/m/n/10 from_dataframe() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (17.1711pt too wide) in paragraph at lines 272--274 \T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 274--276 []\T1/pcr/m/n/10 from_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.w eather.Metadata Underfull \hbox (badness 10000) in paragraph at lines 276--278 []\T1/pcr/m/n/10 from_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 278--280 []\T1/pcr/m/n/10 from_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (17.1711pt too wide) in paragraph at lines 278--280 \T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 ), [31] Underfull \hbox (badness 10000) in paragraph at lines 280--282 []\T1/pcr/m/n/10 FullRisk() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 280--282 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 285--287 []\T1/pcr/m/n/10 generate_demographics() Overfull \hbox (115.97037pt too wide) in paragraph at lines 285--287 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator.Dem ographicsGenerator Underfull \hbox (badness 10000) in paragraph at lines 287--289 []\T1/pcr/m/n/10 generate_metadata() Overfull \hbox (115.97037pt too wide) in paragraph at lines 287--289 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.DemographicsGenerator.Dem ographicsGenerator Overfull \hbox (173.87039pt too wide) in paragraph at lines 289--291 []\T1/pcr/m/n/10 generate_nodes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demo graphics.DemographicsGenerator.DemographicsGenerator Underfull \hbox (badness 10000) in paragraph at lines 291--293 []\T1/pcr/m/n/10 generatePopulation() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e Underfull \hbox (badness 10000) in paragraph at lines 291--293 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 293--295 []\T1/pcr/m/n/10 get_class_with_defaults() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in m od-ule Underfull \hbox (badness 10000) in paragraph at lines 295--297 []\T1/pcr/m/n/10 get_default_campaign_event() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 i n mod-ule Underfull \hbox (badness 10000) in paragraph at lines 297--299 []\T1/pcr/m/n/10 get_node_ids_from_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Overfull \hbox (105.59949pt too wide) in paragraph at lines 299--301 []\T1/pcr/m/n/10 get_nodes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializa tion.SerializedPopulation.SerializedPopulation Underfull \hbox (badness 10000) in paragraph at lines 301--303 []\T1/pcr/m/n/10 get_xpix_ypix() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 303--305 []\T1/pcr/m/n/10 getAttributeValues() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e Underfull \hbox (badness 10000) in paragraph at lines 303--305 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 305--307 []\T1/pcr/m/n/10 getIndividualsWithProperty() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 i n mod-ule Underfull \hbox (badness 10000) in paragraph at lines 305--307 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 307--309 []\T1/pcr/m/n/10 getNextIndividualSuid() Overfull \hbox (77.69946pt too wide) in paragraph at lines 307--309 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation.Ser ializedPopulation Underfull \hbox (badness 10000) in paragraph at lines 309--311 []\T1/pcr/m/n/10 getNextInfectionSuid() Overfull \hbox (77.69946pt too wide) in paragraph at lines 309--311 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation.Ser ializedPopulation Underfull \hbox (badness 10000) in paragraph at lines 311--313 []\T1/pcr/m/n/10 getPropertyValues2() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e Underfull \hbox (badness 10000) in paragraph at lines 311--313 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Overfull \hbox (26.83089pt too wide) in paragraph at lines 317--319 []\T1/pcr/m/n/10 header() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelrepor ts.channels.ChannelReport Underfull \hbox (badness 10000) in paragraph at lines 327--329 []\T1/pcr/m/n/10 id() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.spatialreports.s patial.SpatialNode Underfull \hbox (badness 7308) in paragraph at lines 329--330 []\T1/pcr/m/n/10 id() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.weather. WeatherNode prop- Overfull \hbox (6.84114pt too wide) in paragraph at lines 330--332 []\T1/pcr/m/n/10 id_reference() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weathe r.weather.Metadata Overfull \hbox (1.47115pt too wide) in paragraph at lines 332--334 []\T1/pcr/m/n/10 id_reference() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weathe r.weather.Weather Underfull \hbox (badness 10000) in paragraph at lines 334--336 []\T1/pcr/m/n/10 init_resolution_from_file() Underfull \hbox (badness 10000) in paragraph at lines 334--336 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.Node.Node class Underfull \hbox (badness 10000) in paragraph at lines 336--338 []\T1/pcr/m/n/10 InitAgeUniform() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 336--338 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 338--340 []\T1/pcr/m/n/10 InitPrevUniform() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 338--340 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 340--342 []\T1/pcr/m/n/10 InitRiskUniform() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 340--342 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 342--344 []\T1/pcr/m/n/10 InitSusceptConstant() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le Overfull \hbox (15.62103pt too wide) in paragraph at lines 342--344 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 348--350 []\T1/pcr/m/n/10 lat_lon_from_nodeid() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le Underfull \hbox (badness 10000) in paragraph at lines 350--352 []\T1/pcr/m/n/10 load_default_config_as_rod() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 i n mod-ule Overfull \hbox (31.30106pt too wide) in paragraph at lines 350--352 \T1/ptm/m/it/10 emod_api.config.default_from_schema_no_validation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 352--354 []\T1/pcr/m/n/10 loadInfection() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 352--354 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 360--362 []\T1/pcr/m/n/10 make_config_from_poi() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod- ule Underfull \hbox (badness 10000) in paragraph at lines 360--362 \T1/ptm/m/it/10 emod_api.config.from_poi_and_binary\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 362--364 []\T1/pcr/m/n/10 make_config_from_poi_and_config_dict() Overfull \hbox (16.3614pt too wide) in paragraph at lines 362--364 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule emod_api.config.from_poi_and_binary\ T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 364--366 []\T1/pcr/m/n/10 make_config_from_poi_and_config_file() Overfull \hbox (16.3614pt too wide) in paragraph at lines 364--366 \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule emod_api.config.from_poi_and_binary\ T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 366--368 []\T1/pcr/m/n/10 make_config_from_poi_and_schema() \T1/ptm/m/n/10 (\T1/ptm/m/it /10 in Overfull \hbox (3.35153pt too wide) in paragraph at lines 366--368 \T1/ptm/m/it/10 mod-ule emod_api.config.from_poi_and_binary\T1/ptm/m/n/10 ), [32] Underfull \hbox (badness 10000) in paragraph at lines 369--370 []\T1/pcr/m/n/10 metadata() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather.we ather.Weather Underfull \hbox (badness 10000) in paragraph at lines 370--371 []\T1/pcr/m/n/10 MigrationFile \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Overfull \hbox (2.6225pt too wide) in paragraph at lines 377--378 []| \T1/pcr/m/n/10 emod_api.config.default_from_schema\T1/ptm/m/n/10 , Overfull \hbox (86.6225pt too wide) in paragraph at lines 378--379 []| \T1/pcr/m/n/10 emod_api.config.default_from_schema_no_validation\T1/ptm/m/n /10 , Overfull \hbox (56.6225pt too wide) in paragraph at lines 379--380 []| \T1/pcr/m/n/10 emod_api.config.dtk_post_process_adhocevents\T1/ptm/m/n/10 , Overfull \hbox (50.6225pt too wide) in paragraph at lines 380--381 []| \T1/pcr/m/n/10 emod_api.config.dtk_pre_process_adhocevents\T1/ptm/m/n/10 , Overfull \hbox (8.6225pt too wide) in paragraph at lines 381--382 []| \T1/pcr/m/n/10 emod_api.config.dtk_pre_process_w5ml\T1/ptm/m/n/10 , Overfull \hbox (2.6225pt too wide) in paragraph at lines 383--384 []| \T1/pcr/m/n/10 emod_api.config.from_poi_and_binary\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 387--388 []| \T1/pcr/m/n/10 emod_api.demographics.demographics\T1/ptm/m/n/10 , Overfull \hbox (20.6225pt too wide) in paragraph at lines 388--389 []| \T1/pcr/m/n/10 emod_api.demographics.DemographicsFile\T1/ptm/m/n/10 , Overfull \hbox (50.6225pt too wide) in paragraph at lines 389--390 []| \T1/pcr/m/n/10 emod_api.demographics.DemographicsGenerator\T1/ptm/m/n/10 , Overfull \hbox (92.6225pt too wide) in paragraph at lines 390--391 []| \T1/pcr/m/n/10 emod_api.demographics.DemographicsInputDataParsers\T1/ptm/m/ n/10 , Overfull \hbox (50.6225pt too wide) in paragraph at lines 391--392 []| \T1/pcr/m/n/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 , Overfull \hbox (44.6225pt too wide) in paragraph at lines 395--396 []| \T1/pcr/m/n/10 emod_api.examples.serialized_file_mc_to_sc\T1/ptm/m/n/10 , Overfull \hbox (20.6225pt too wide) in paragraph at lines 399--400 []| \T1/pcr/m/n/10 emod_api.interventions.import_pressure\T1/ptm/m/n/10 , Overfull \hbox (14.6225pt too wide) in paragraph at lines 401--402 []| \T1/pcr/m/n/10 emod_api.interventions.simple_vaccine\T1/ptm/m/n/10 , Overfull \hbox (26.6225pt too wide) in paragraph at lines 405--406 []| \T1/pcr/m/n/10 emod_api.schema.dtk_post_process_schema\T1/ptm/m/n/10 , Overfull \hbox (14.6225pt too wide) in paragraph at lines 409--410 []| \T1/pcr/m/n/10 emod_api.serialization.dtkFileSupport\T1/ptm/m/n/10 , Overfull \hbox (2.6225pt too wide) in paragraph at lines 410--411 []| \T1/pcr/m/n/10 emod_api.serialization.dtkFileTools\T1/ptm/m/n/10 , Overfull \hbox (14.6225pt too wide) in paragraph at lines 411--412 []| \T1/pcr/m/n/10 emod_api.serialization.dtkFileUtility\T1/ptm/m/n/10 , Overfull \hbox (50.6225pt too wide) in paragraph at lines 412--413 []| \T1/pcr/m/n/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 418--420 []\T1/pcr/m/n/10 MortalityRateByAge() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul e Overfull \hbox (15.62103pt too wide) in paragraph at lines 418--420 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Overfull \hbox (15.62103pt too wide) in paragraph at lines 420--422 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 425--427 []\T1/pcr/m/n/10 new_intervention() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 425--427 \T1/ptm/m/it/10 emod_api.interventions.import_pressure\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 427--429 []\T1/pcr/m/n/10 new_intervention() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 429--431 []\T1/pcr/m/n/10 new_intervention() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 429--431 \T1/ptm/m/it/10 emod_api.interventions.simple_vaccine\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 431--433 []\T1/pcr/m/n/10 new_intervention_as_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 433--435 []\T1/pcr/m/n/10 new_intervention_as_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 435--437 []\T1/pcr/m/n/10 new_intervention_as_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (32.8303pt too wide) in paragraph at lines 438--440 []\T1/pcr/m/n/10 node_count() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.spatialr eports.spatial.SpatialReport Underfull \hbox (badness 10000) in paragraph at lines 442--444 []\T1/pcr/m/n/10 node_count() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather. weather.Weather Underfull \hbox (badness 10000) in paragraph at lines 444--446 []\T1/pcr/m/n/10 node_ID_from_lat_long() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod -ule Overfull \hbox (46.65079pt too wide) in paragraph at lines 444--446 \T1/ptm/m/it/10 emod_api.demographics.DemographicsInputDataParsers\T1/ptm/m/n/1 0 ), Overfull \hbox (20.8303pt too wide) in paragraph at lines 446--448 []\T1/pcr/m/n/10 node_ids() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 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[]\T1/pcr/m/n/10 NoRisk() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Overfull \hbox (15.62103pt too wide) in paragraph at lines 467--469 \T1/ptm/m/it/10 emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/10 ), Overfull \hbox (62.83089pt too wide) in paragraph at lines 469--471 []\T1/pcr/m/n/10 num_channels() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channe lreports.channels.ChannelReport Overfull \hbox (31.71117pt too wide) in paragraph at lines 471--473 []\T1/pcr/m/n/10 num_channels() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channe lreports.channels.Header Overfull \hbox (74.83089pt too wide) in paragraph at lines 473--475 []\T1/pcr/m/n/10 num_time_steps() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.chan nelreports.channels.ChannelReport Overfull \hbox (43.71117pt too wide) in paragraph at lines 475--477 []\T1/pcr/m/n/10 num_time_steps() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.chan nelreports.channels.Header Underfull \hbox (badness 10000) in paragraph at lines 480--482 []\T1/pcr/m/n/10 printParameters() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 480--482 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 484--486 []\T1/pcr/m/n/10 provenance() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.weather. weather.Weather Overfull \hbox (1.84042pt too wide) in paragraph at lines 491--492 []\T1/pcr/m/n/10 read() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule emod_api.ser ialization.dtkFileTools\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 493--495 []\T1/pcr/m/n/10 recurser() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 493--495 \T1/ptm/m/it/10 emod_api.schema.dtk_post_process_schema\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 495--497 []\T1/pcr/m/n/10 removeIndividuals() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 495--497 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 497--499 []\T1/pcr/m/n/10 removeNumberIndividuals() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in m od-ule Underfull \hbox (badness 10000) in paragraph at lines 497--499 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Overfull \hbox (56.83089pt too wide) in paragraph at lines 499--501 []\T1/pcr/m/n/10 report_type() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channel reports.channels.ChannelReport Overfull \hbox (25.71117pt too wide) in paragraph at lines 501--503 []\T1/pcr/m/n/10 report_type() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channel reports.channels.Header Overfull \hbox (74.83089pt too wide) in paragraph at lines 503--505 []\T1/pcr/m/n/10 report_version() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.chan nelreports.channels.ChannelReport Overfull \hbox (43.71117pt too wide) in paragraph at lines 505--507 []\T1/pcr/m/n/10 report_version() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.chan nelreports.channels.Header Overfull \hbox (4.77174pt too wide) in paragraph at lines 507--509 []\T1/pcr/m/n/10 res_in_degrees \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demogr aphics.Node.Node Underfull \hbox (badness 10000) in paragraph at lines 513--515 []\T1/pcr/m/n/10 SchemaConfigBuilder \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 515--517 []\T1/pcr/m/n/10 SchemaConfigBuilder \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 517--519 []\T1/pcr/m/n/10 serialized_dtk_to_json() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo d-ule Underfull \hbox (badness 10000) in paragraph at lines 517--519 \T1/ptm/m/it/10 emod_api.examples.serialized_file_mc_to_sc\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 519--521 []\T1/pcr/m/n/10 SerializedPopulation \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 519--521 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 521--523 []\T1/pcr/m/n/10 SerialObject \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 523--525 []\T1/pcr/m/n/10 set_demog_distributions() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in m od-ule Underfull \hbox (badness 10000) in paragraph at lines 523--525 \T1/ptm/m/it/10 emod_api.demographics.demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 525--527 []\T1/pcr/m/n/10 set_growing_demographics() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 527--529 []\T1/pcr/m/n/10 set_immune_mod() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 527--529 \T1/ptm/m/it/10 emod_api.demographics.demographics\T1/ptm/m/n/10 ), Overfull \hbox (173.87039pt too wide) in paragraph at lines 529--531 []\T1/pcr/m/n/10 set_resolution() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demo graphics.DemographicsGenerator.DemographicsGenerator Underfull \hbox (badness 10000) in paragraph at lines 531--533 []\T1/pcr/m/n/10 set_risk_mod() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 531--533 \T1/ptm/m/it/10 emod_api.demographics.demographics\T1/ptm/m/n/10 ), Overfull \hbox (16.62106pt too wide) in paragraph at lines 533--535 []\T1/pcr/m/n/10 set_schema() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.schema_t o_class.ReadOnlyDict Underfull \hbox (badness 10000) in paragraph at lines 535--537 []\T1/pcr/m/n/10 set_schema() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 535--537 \T1/ptm/m/it/10 emod_api.config.from_poi_and_binary\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 537--539 []\T1/pcr/m/n/10 set_static_demographics() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in m od-ule Underfull \hbox (badness 10000) in paragraph at lines 537--539 \T1/ptm/m/it/10 emod_api.demographics.demographics\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 539--541 []\T1/pcr/m/n/10 setAttribute() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 539--541 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), [34] Underfull \hbox (badness 10000) in paragraph at lines 541--543 []\T1/pcr/m/n/10 setAttributes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 541--543 \T1/ptm/m/it/10 emod_api.serialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 543--545 []\T1/pcr/m/n/10 setIndividualPropertyInfections() \T1/ptm/m/n/10 (\T1/ptm/m/it /10 in Overfull \hbox (25.39023pt too wide) in paragraph at lines 543--545 \T1/ptm/m/it/10 mod-ule emod_api.serialization.SerializedPopulation\T1/ptm/m/n/ 10 ), Overfull \hbox (36.30013pt too wide) in paragraph at lines 545--547 []\T1/pcr/m/n/10 show() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule emod_api.ser ialization.SerializedPopulation\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 547--549 []\T1/pcr/m/n/10 SimpleSusceptibilityDistribution() \T1/ptm/m/n/10 (\T1/ptm/m/i t/10 in Overfull \hbox (46.96086pt too wide) in paragraph at lines 547--549 \T1/ptm/m/it/10 mod-ule emod_api.demographics.DemographicsTemplates\T1/ptm/m/n/ 10 ), Overfull \hbox (34.70026pt too wide) in paragraph at lines 549--551 []\T1/pcr/m/n/10 simulation() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializ ation.dtkFileTools.DtkFileV1 Overfull \hbox (34.70026pt too wide) in paragraph at lines 551--553 []\T1/pcr/m/n/10 simulation() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializ ation.dtkFileTools.DtkFileV2 Overfull \hbox (34.70026pt too wide) in paragraph at lines 553--555 []\T1/pcr/m/n/10 simulation() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serializ ation.dtkFileTools.DtkFileV3 Overfull \hbox (2.94016pt too wide) in paragraph at lines 555--556 []\T1/pcr/m/n/10 Snappy \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in emod_api.seria lization.dtkFileSupport\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 556--557 []\T1/pcr/m/n/10 SpatialNode \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Underfull \hbox (badness 10000) in paragraph at lines 557--559 []\T1/pcr/m/n/10 SpatialReport \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in Overfull \hbox (50.83089pt too wide) in paragraph at lines 559--561 []\T1/pcr/m/n/10 start_time() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelr eports.channels.ChannelReport Overfull \hbox (19.71117pt too wide) in paragraph at lines 561--563 []\T1/pcr/m/n/10 start_time() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelr eports.channels.Header Overfull \hbox (91.05998pt too wide) in paragraph at lines 563--565 []\T1/pcr/m/n/10 STATIC \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographics.D emographicsGenerator.DemographicsType Overfull \hbox (44.83089pt too wide) in paragraph at lines 565--567 []\T1/pcr/m/n/10 step_size() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelre ports.channels.ChannelReport Overfull \hbox (13.71117pt too wide) in paragraph at lines 567--569 []\T1/pcr/m/n/10 step_size() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelre ports.channels.Header Overfull \hbox (50.83089pt too wide) in paragraph at lines 574--576 []\T1/pcr/m/n/10 time_stamp() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelr eports.channels.ChannelReport Overfull \hbox (19.71117pt too wide) in paragraph at lines 576--578 []\T1/pcr/m/n/10 time_stamp() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelr eports.channels.Header Overfull \hbox (32.8303pt too wide) in paragraph at lines 578--580 []\T1/pcr/m/n/10 time_steps() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.spatialr eports.spatial.SpatialReport Underfull \hbox (badness 5741) in paragraph at lines 580--582 []\T1/pcr/m/n/10 title() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.channelreport s.channels.Channel Underfull \hbox (badness 10000) in paragraph at lines 582--583 []\T1/pcr/m/n/10 to_dict() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographic s.Node.Node Overfull \hbox (161.87039pt too wide) in paragraph at lines 583--585 []\T1/pcr/m/n/10 to_grid_file() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demogr aphics.DemographicsGenerator.DemographicsGenerator Overfull \hbox (10.96092pt too wide) in paragraph at lines 585--587 []\T1/pcr/m/n/10 to_json() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.migration.m igration.MigrationFile Underfull \hbox (badness 10000) in paragraph at lines 587--588 []\T1/pcr/m/n/10 to_tuple() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.demographi cs.Node.Node Underfull \hbox (badness 10000) in paragraph at lines 588--590 []\T1/pcr/m/n/10 tool() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 emod_api.serialization. dtkFileTools.DtkFile Overfull \hbox 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(./institute-for-disease-modeling-emod-api.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on institute-for-disease-modeling-emod-api.pdf (40 pages, 203565 bytes). 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